Missing in Action
by Belisse
Summary: [COMPLETE]The Genii had a plan, they will get back at the people from Atlantis at any cost. Please R
1. Prologue

T**itle: Missing in Action**

**Author: Belisse**

**Archive: Any other out there, just ask first.**

**Fandom: Stargate Atlantis**

**Category: H/C**

**Rating: R**

**Summary: The Genii had a plan, they will get back at the people from Atlantis at any cost.**

**Warnings: Angst, violence, language, torture.**

**Beta: Falcon Horus**

**Season/Episode: Season One**

**Spoilers: Everything concerning the Genii**

**Disclaimer: As much as I wanted, SGA is not mine and will never be. This is just for fun.**

Prologue

The pupil rose from the floor, the master was pleased. This new student had proven himself a worthy fighter. Acastus Kolya knew that his new student couldn't yet be fully trusted, but time was of the essence. He would finally have his revenge on the people of Atlantis.

The student was now waiting for the orders of his master, Kolya looked at him, "You're dismissed! Be ready, tonight is really important. Tonight you will show your loyalties to me." Kolya was answered by a quick "Yes sir." The student bowed and left for his quarters.

As the student left, Kolya smiled to himself, sure that he will get his ultimate revenge. Tonight he will make amends with the Genii council; tonight he will kill Major John Sheppard.

-0-

The strike was going as planned, the Intel the Genii had gathered had been correct. The people of Atlantis were on this planet to continue their pitiful acts of trade. The group moved into the village quite easy as most of the people had gathered in the center of the town.

Kolya had his new student close to him, he would know death soon enough. The strike team didn't care who was in the way; people were either stunned or killed before an alarm could be raised.

Once they arrived where most people were gathered, Kolya stopped the team and looked at his student, "You know what to do. We will cover you. If we get separated, just return home."

The student nodded, weapon at hand, he moved into the big plaza. He spotted the ones he was looking for quite easily. He waited, something inside him wanted to stop what he was about to do; murder. Could he live with that?

Yes! He was of the Genii, people who were proud of what they were, and the ones he wanted dead were nothing but terrorists. So the student walked onto the plaza, weapon ready to use. He shot the first one on his path; Rodney McKay went down without so much as a peep.

Next in line he saw Teyla, the place had now become invaded by a panicked mob. People were trying to run away from the sole attacker, hiding in surrounding homes.

As he approached, Teyla spotted him; her eyes were wide with shock. He fired the weapon. He missed, her reflexes were quick, and Teyla evaded the hit and took off. The student quickly followed her and entered through the first open door that was in his path. Lt. Ford was next in sight, his weapon at the ready. The student fired his weapon but Ford managed to hide behind a table.

His mind was now on overload, somehow he didn't wanted to do this, but he would do it nonetheless. No one was shooting at him, which was strange; but his commander was close behind him.

But to really prove himself to commander Kolya he had to kill the team from Atlantis himself. He moved and spotted Ford; again he fired his weapon without success. His patience was running low; he closed in where Ford was hiding.

Ford was caught off guard. The two men stared at each other; rage filled the student's face. Ford's face was a mixture of shock and amazement. Both men were ready to shoot each other.

Without warning Teyla appeared and slammed the butt of her P90 on the student's head. The man fell to the floor unconscious, Teyla and Ford stared at each other almost in shock. Before they could say anything, all hell broke loose when the rest of the Genii strike team entered the plaza.

The leader of the village approached Ford; he had sent his guard to hold off the attacker, while he helped them get back to the Stargate.

The battle was now in the distance; Ford and Teyla were accompanied by Oles, the leader of the village. Four guards accompanied them, by carrying two limp bodies back to the Stargate.

Once there, Teyla dialed the gate, once the wormhole was established Ford dialed his IDC sequence and without hesitation everyone stepped through the event horizon.

On the other side the two bodies where placed on the floor. Dr. Elizabeth Weir ran down the stairs and glanced at the team. She looked around and saw McKay who was now receiving medical attention.

To his side laid the unconscious body of Major John Sheppard, who was reported missing in action for a little over four months ago.


	2. Make me Bad

**Make me Bad**

Elizabeth Weir had been up all night, trying to figure out how her ranking military officer had suddenly and without obvious reason appeared right at the exact location the team from Atlantis. More importantly, why Sheppard had tried to kill them? She had gone to the infirmary earlier to see how Rodney was doing. Carson told her that the bullet had missed major organs and with a bit of rest he would be his old self again in a couple of weeks.

John, however, was another matter. She didn't want to think about what kind of things he must have gone through. Especially, what had been done to him which turned John against his own people. There was something very wrong with all of this.

She had read the report from that unfortunate day four months ago for the umpteenth time by now and still the facts were eluding her. Elizabeth massaged her temples as she remembered the moment the team came through the gate and John wasn't with them. They had been running for their lives and something had gone terribly wrong. The search and rescue came up empty handed, it had been pointless ... he had disappeared without trace.

Her thoughts were interrupted at once as she heard the radio crackle to life, "Dr. Weir?"

"Yes Carson?"

"He's awake."

If Elizabeth was completely honest to herself, she really didn't want to see John at this moment. She knew that the person she was now on her way to see would not act like the John she had known before that mission four months ago. Worse even, he most likely wouldn't regret having shot Rodney.

As she arrived at the infirmary, Elizabeth didn't need to ask why everyone outside had an expression as if someone had died. John's angry screams could be heard from a mile away, and they weren't of the friendly kind either.

"You have no right for keeping me here! Let me go now! I fucking swear the moment I have the opportunity I will rip everybody's head off!"

_Colorful_… Elizabeth sighed heavily before walking inside. Carson was standing next to Rodney's bed, checking his vitals, when he noticed Elizabeth walking in. He gave her a nod, acknowledging her presence. Once Elizabeth came into John's view he shut up.

He stared at Elizabeth for a second, giving her a once over, "Oh… you." And immediately dropped his head back on the pillow.

His behavior shocked her a little as she watched him, finally able to examine the former ranking military officer. He looked thinner while his hair was no longer consisting of sprays of spiked strands and he had grown a beard. For some reason the man in front of her didn't look anything like the John Sheppard she remembered, and still he was that same John, just different. He had been restrained to the bed, probably the reason why he had been screaming earlier. Elizabeth could see blisters forming around his wrists and ankles.

"Hello." She finally made the first move. Unable to move much, John lifted his head and stared at her, while she simply continued, "What happened, John?"

He smirked, a cruel one no less, "That is not my name. I am Ignatius of the Genii and I demand you to release me!"

His new persona had finally come into the open, "Well… Ignatius, you attempted to murder three of my people. I have all the rights to keep you like this forever."

He gave her a hard stare back, "Then our conversation is over."

Elizabeth felt a rush of anger taking control of her body, "No, this is not over. You are Major John Sheppard and I demand you to explain your actions." Elizabeth couldn't believe the sudden strength that caused her to yell at the man in front of her. She successfully tried to show her seriousness of the situation on her face.

But John's face was riddled with smugness. "My actions are nothing more than the noble work of the Genii and if you are not here to talk about my release, then I suggest you leave. Because your pathetic attempts of interrogation are quite boring."

Elizabeth couldn't believe what he just said. Right at that moment she actually believed that the man in front of her wasn't the Sheppard she used to know. Elizabeth decided that retreat was now the best option. She quickly turned around and walked towards Carson, who was still standing next to Rodney, "Let me know when Rodney wakes up." Carson nodded and Elizabeth walked out of the infirmary, holding back a few stray tears.

The moment she stepped outside she could feel all eyes upon her at once and she knew she now had to face the rest of the team waiting outside. Once Lt. Ford saw Dr. Weir, he immediately wanted to know everything she could tell them.

"Lieutenant, let us take this up to the briefing room. Shall we say in ten minutes?" Ford nodded eagerly. "There we can decide on what to do next."

Elizabeth excused herself and left the rest of the team at the infirmary, knowing they would soon enough follow her towards the briefing room. As she made her way over there, she relived the events of that faithful day four months ago. She recalled being in the briefing room when the call of Sheppard's team coming in hot had come.

She had quickly been summoned to the control room. And as she had been waiting to ask the inevitable question '_What on earth happened this time?'_, Rodney and Teyla had come running through the event-horizon first, closely followed by Ford. All of them stopping at once, turning back to the open wormhole waiting for John to appear, but he never did and the gate shut down crushing almost every hope he might still be alive.

Ford had quickly informed her about the situation they had gotten themselves into. They had been attacked by what had looked like natives.

Elizabeth sent 3 teams, risking the fact they could all be attacked and possibly killed, but neither one of them had found one living being. It looked like Major John Sheppard had just vanished into thin air.

A month or so after that, they had searched the planet again and still there had been no signs of anything, not even natives. Which was extremely weird and now Elizabeth Weir knew why no one had been found on that particular planet. She knew now, that there were no natives, only the Genii. One of the few things she couldn't figure out was how the Genii knew they were going to be on this planet at that moment in time.

This brought her back to the matter at hand, determining John's liability to himself and decide what to do with him. It wasn't like Atlantis had its own mental facility. They did have a psychologist, Dr. Heightmeyer, but she wasn't sure the woman could help. She knew that eventually John would end up in the same cell they had used to keep the Wraith he so affectionately had named Steve.

-0-0-0-

Lt. Ford, Teyla and Sgt. Bates, who Elizabeth had contacted during her own walk towards the briefing room, quietly entered the room. She was already sitting in her usual chair. As soon as they were all seated they knew they had only one thing to discuss, what to do with Major Sheppard.

Carson came in a few seconds after the others, quietly taking a seat of his own. Elizabeth stared at the doctor, "How are Dr. McKay and ... the Major doing?"

"Rodney will be fine; we just need to regularly check his wound, so it doesn't develop an infection." Carson replied tiredly, dark circles forming under his eyes.

"What about the Major?" Asked Lt. Ford.

Carson turned grim, "We have him sedated at the moment. After you left he became a bit more violent. As for his mental status, he's definitely under some sort of mind control."

Elizabeth had been expecting this, "What about his physical health?"

"He's thinner, but he's not malnourished or dehydrated. I did a full check up and there are no drugs or chemicals in his blood. He doesn't have scars or marks of any type, so I doubt he was tortured physically. Everything they did was screw up his mind. And to be honest, that can be more devastating than physical torture."

This was Bates' time to chime in, "Dr. Weir, I would recommend putting him in one of the holding cells, at least for the time being."

Elizabeth nodded, "I've already thought of it. Once you get Carson's okay, you can see to it."

"Yes ma'am." Bates nodded, knowing he would do anything to keep the rest of Atlantis safe from the now maniacal Major.

Elizabeth then turned her attention to Ford and Teyla, "I am going to need both your help. I need you to take your time and talk to him. Nothing much, just to see what we can get out of him."

Ford answered promptly, "Yes Ma'am."

Teyla stared at Elizabeth, "How long do you think he will be like this?"

Carson glanced from Elizabeth to Teyla, "If we don't do anything about it, he could be like this forever."

Elizabeth turned to Teyla, "When you go see him, talk to him as a friend. Remind him of good times and simple things. Things that you know meant something to him. You don't have to do it right away, but once you do it let me know how it went. And that applies for all of you. Dismissed."

Sgt. Bates and Carson left the room together while Teyla and Ford stayed behind a little. "Dr. Weir, do you think we can bring him back?" Ford looked at her, searching for something, maybe reassurance that everything would be okay again.

Elizabeth gave the young Lieutenant's question some serious thought before looking back at him. She really wished she could tell him everything would be fine but she couldn't know for sure. She had doubts too. "I don't know, but at least we can try. I am not ready to give up on him just yet. No matter how big mouthed he has become."

Teyla stood up from her chair, "Do not worry Dr. Weir, we are not giving up on him either."

Elizabeth nodded and Teyla and Ford retreated out of the briefing room, leaving her to her own private thoughts.

Elizabeth really wished everything was going to be ok. But somewhere in the back of her mind something was poking at the possibility that hell was about to break loose and they wouldn't be able to stop it.

-0-0-

Rodney woke up with a sudden feeling of being completely lost. _Where am I? Ok, obviously back in Atlantis. Then why am I in the infirmary? And why do I hurt so much? What happened to me?_ His last memories were of being off world. He was having a small conversation with someone from the nearby town, when he felt an incredible pain in his back. Which was like the last memory he could find that made some sense to him.

So now he was lying in the infirmary of Atlantis and all he could hear were Sheppard's angry screams. _Wait, is that Sheppard?_ He heard another round of really strong curses coming out of John's very mouth. _What is it with him? _

Rodney tried to move but his chest and back hurt at the same time. Then Carson came into view, he was looking a bit shaken, but smiled when he saw Rodney awake.

As Carson moved towards Rodney, John's screams died down. Rodney safely assumed that John had been given the sleeping potion.

"Hey Rodney, how are you feeling?"

Rodney looked at Carson, "It hurts." The doctor was now looking absent minded to the monitor besides Rodney's bed, "You'll be fine, the bullet went in and out, and it missed major organs. As I said, you will be fine."

"Bullet wound? What the hell happened to me?" Rodney asked frowning.

"You were shot."

As simple as the answer was, Rodney couldn't fathom who shot him. Though he could tell from the way Carson looked at him he was not going to like the answer of his next question, "Who shot me?"

Carson waited for a moment, not sure if he should answer, "Major Sheppard."

"What?" Rodney looked at him in shock. "Sheppard was declared MIA, possibly KIA, four months ago!" Then his shock turned into suspicion. "Why would he want to kill me?"

"We think he was brainwashed by the Genii." Carson replied grimly.

Rodney looked around. "So… that's why he was so…"

"Big mouthed? Yeah, I know."

Rodney tried to sit, but his body didn't allow it. Carson placed a hand on his shoulder, preventing him from doing just that even though he knew the body would already be screaming not to sit upright.

"Let me get you something for the pain." Carson walked away, leaving Rodney to wonder about how things in Atlantis couldn't get any weirder. He had no idea how wrong he was.


	3. Down with the Sickness

**Down with the Sickness**

_John… how dare she call me John? My name is Ignatius… yes; Ignatius has always been my name. John Sheppard was only my spy name._

It was as if the man was trying to convince himself he was in fact someone else than this John. He lay on his bed, his wrists and ankles sore from pulling the restraints. He also felt extremely groggy, knowing whatever the damned doctor had given him, and it was meant to knock you out for quite a while.

But he was sure that once the right opportunity presented itself to him, he would have the pleasure of killing all these people. He would return to his people victoriously and he would hand Atlantis to Commander Kolya, whose pride he would earn.

He tried to move again but the restraints had been closed tight against his skin. They had some sort of cushion in order to protect the one inside the restraints against unnecessary wounds but still his skin had turned all red.

Ignatius didn't know how much time he had spent lying there, but one thing he did know was that the people here were practically ignoring him, which bugged him to no end. Then he heard someone whispering near him, they were talking about him. The voices got stronger the closer they came. The Doctor who had sedated him earlier had returned along with two soldiers he vaguely remembered had been addressed as Ford and Bates.

Bates closed in on his bed, slow enough and calculating every possible move the Major could make that could put them all in some form of danger. "We're moving you, Major. Be warned that if you try anything we won't hesitate to stun you, more than once if necessary."

John, now known as Ignatius or so he thought, didn't have a clue of what Bates meant by stunning him more than once. But glancing at the guns triggered a memory he had stored in his mind of being hit by one of those once, remembering it hadn't been all too pleasant. Not that weapons were supposed to be pleasant.

The Doctor approached him and started to loosen the restraints. His hands were first, followed by his legs, while the soldiers were both pointing their large guns at him.

He got up slowly, his body aching a bit of lying so long on the bed. He winced but kept his mouth shut, not wanting to alert that Doctor again. He wasn't in the mood for another round of sedatives, which prevented him from completing his ultimate goal. Bates ordered him to move toward the exit, which he followed thinking at the same time how easy it would be to escape victoriously.

As they passed the other bed, he took a glance and saw McKay sitting in it. Both men stared at each other and John snorted loudly. Damn it! The only one that I manage to shoot and he lives!

Near the door he saw the opportunity he had been looking for since the moment he had been planning on getting out of there. The space was less crammed near the exit, which resulted in one soldier in front of him and another behind him.

The Doctor was walking close by, though keeping his distance a little. Knowing the man they knew as John, couldn't be trusted at this point. Without attracting too much attention Ignatius closed in on Ford. And just as they thought everything was going as planned he grabbed Ford's 9mm, turned around and shot Bates.

Ignatius quickly made it to the Doctor's side, which he used as a shield just at the exact moment Ford shot at him with his stunner, hitting the Doctor instead of his intended target.

The moment the stun hit Dr. Beckett he fell to the floor unconscious.

Ford aimed again, trying a second time to stun his target but this time John shielded himself behind a bed.

From under it, he could see Ford's legs closing in. Having a clear shot he fired the 9mm, hitting Ford in the left leg. Ignatius crawled towards Bates and grabbed his stunner, realizing such a weapon could come in handy around Atlantis. Even though his objective was to kill he was sure he could pleasure his master with a greater gift then just the death of all the expedition members.

He got up quickly, stunning Ford as he did so and gave Bates an extra stun just in case. He turned around to look at what he had done, grinned widely and then ran off, away from the infirmary and in the direction of the one place he knew he would be at the greatest risk of being apprehended again, but he wouldn't let it come that far. He was absolutely sure he would make it back to his master.

-0-0-0-

Elizabeth was in her office, her head buried in her hands, fighting to keep her eyes from closing and her body from taking that extra sleep now as she sat behind her desk. Realizing she was loosing the fight with sleep, she carelessly plucked the radio out of her ear and let it hang. A really bad headache was filling her brain and she knew the only thing that could cure that pain was a good night's sleep. She wasn't sure though she could get that at this very bad moment. For a moment she let her body take over, allowing it a second of rest but also knowing she had to continue her work. John was too important and he would need all the help they could give him.

She had to be strong; after all she was the leader of the expedition. She couldn't allow herself to show weakness, not towards her colleagues and certainly not towards the Major. Elizabeth took a deep breath and let it out slowly before putting the radio back into her ear, just in time to hear Rodney shouting something through it. Wait a second! Rodney is still in the infirmary. Why is he...?

"Rodney?"

"Elizabeth, Major Sheppard escaped from the infirmary, I think he might make his way toward the gate room." Rodney was barely finished when she heard the gate being activated. Knowing the wormhole was an outgoing one and the one activating it wasn't supposed to dial out in the first place, Elizabeth got up and quickly left her office.

What happened next almost went in slow motion. She felt a tingling sensation hitting her body and mind, and before she fully realized what had happened to her she found herself being taken over by pure blackness.

Elizabeth's limp body fell to the floor with a soft thud. Ignatius took a second to look her over and then picked her up from the floor, swinging her over his shoulder. The open Stargate was waiting for him and he had to hurry if he wanted his plan to succeed. A large smile crept onto his features, realizing he would be going home in just a few seconds.

He realized too late however what was happening around him. He was barely at the Gate when he was hit with enough stunners to bring down an elephant. The last thought was one of pure hatred ... he would get his revenge one way or another.


	4. Papercut

Papercut

Pins and needles were all he could feel, while for a moment only the room around him changed. He was lying on a table, his wrists and legs tied to it. It was a large room, damp and a bit dark; the only source of light a small window near one of the corners. But it wasn't enough to light up the entire space he was in, leaving him in the dark quite literally.

He tried to move his head in order to have a little look around but something was placed on either side of his head, preventing him from moving. As he heard steps coming his way he strained himself to see who it was but the device keeping his head in place didn't give him that much leeway.

A deep voice suddenly spoke from the dark, "Do it."

All he could do next was scream; scream out the pain that was searing through his entire body.

-0-0-0-

Lt. Aiden Ford awoke with the familiar feeling of pins and needles, including an explosion of pain in his left thigh near his knee. He looked around, founding himself in a full infirmary, nurses and others alike buzzing around going from bed to bed. To be quite honest, Aiden didn't remember seeing the infirmary this full ... ever.

Ford straightened himself a little to have a better look. To his right he noticed a nurse putting some new bandages to Bates' shoulder. Behind Bates, Carson was arguing with a nurse, assuring her that he was alright, while he walked around checking on the patients.

To his left laid a couple of the gate room technicians, Peter included, and on the far end Elizabeth Weir.

'_Oh damn, what the hell happened?' _Was the first thought that came to Ford's mind. He noticed Dr. Beckett approached him and gave him a small nod. "How are you feeling, lad?"

Ford was not sure but replied nonetheless, "Like hell! Who else is injured?"

Dr. Beckett looked around, "Well, you and Sgt. Bates were the ones with the more serious wounds. The rest of the people here were either stunned or knocked unconscious."

"Major Sheppard?"

"He was placed in one of the holding cells. Apparently he tried to take Dr. Weir to the Genii. But he got stunned before he could go anywhere near the Gate." Carson said, while he started checking Ford's injury.

It had truly been a close call and if it hadn't been for those who had acted quickly, Atlantis would have been swamped by Genii. Having had a clear advantage on them, them being caught off guard and all, the Major had had the whole city as a playground for moment.

Ford started to feel guilty; after all it had been his gun that had started all this in the first place. He should have been more careful and less trusting towards the Major.

In a flash he recalled the events that had occurred leading up to this last event. If he had only paid more attention to his instincts, he wouldn't have had to deal with a brainwashed CO right about now.

He should have informed Major Sheppard the moment he felt they were being watched. That day he must have checked the life signs detector for the umpteenth time; his senses had been on high alert all morning.

"Calm down Lieutenant, there's nothing here." John Sheppard had told him for the third time.

He should have said it, right at that moment, but he decided to let go of his unsettling feeling, "Yes sir. It's just not a bad thing to be a bit paranoid."

The Major had nodded and walked off towards McKay, "Anytime you feel like finishing!"

McKay, who had been digging in the ground nearby, stopped for a second to stare at Sheppard, "Major, there are strange readings here."

"ZPM kind of readings?"

"I don't know, but it could be a power source of some kind that we have yet to discover."

Ford could really feel the Major loosing his patience real quickly, "I don't see any signs of anything here Rodney, let somebody else deal with this boring planet."

"Do I have to remind you how much we need a strong power source?"

"I get it McKay, just make up your mind and hurry up so we can leave."

Ford had chuckled softly. He sometimes found the ranting between the scientist and the Major quite amusing. At that moment he had decided it would be for the best to join Teyla, who had been looking rather on edge. "Teyla, you okay?"

"Not really. I would like us to leave this planet as soon as possible." Teyla had looked at him, an almost invisible fear imbedded in her eyes. "It's as if we're being watched."

"I know. I'm not feeling comfortable either. I have been spotting some movements right behind the tree line over there." He had pointed in the direction of the trees and Teyla had followed his directions, squeezing her eyes half shut to get a better view.

"You think animals?" Teyla kept her focus upon the tree line.

Ford glanced down at the life signs detector yet again, "I'm not picking anything up. Maybe that area is out of range, but I better inform the Major." Ford had turned to leave but hadn't made it five steps away from Teyla when he had felt himself being pushed aside.

A small dart had brushed his shoulder, which could only mean trouble in the largest sense of the word. Teyla had looked up and had shouted, "Major Sheppard we must leave, we must leave now."

Ford turn to look in the direction the dart had originated from and had quickly spotted the movement he had thought seeing earlier. He turned to face Sheppard, "Unfriendlies at six o'clock!"

Sheppard stared at the tree line and back to his team, "Back to the Stargate! Now!"

Everyone turned at once and ran down the hill as fast as their legs could carry them. In minutes the place where they had been standing was covered in arrows, now stuck in the ground. Ford had heard battle cries in the distance, if they hadn't moved more quickly things could have been a lot uglier.

By the time Ford had reached the stargate, McKay and Teyla had already activated the wormhole. He had been alongside the Major when he had suddenly turned to the Major, "Go, I'll cover you." Sheppard yelled at him.

Ford followed the order blindly and ran with all the strength he had left towards the Stargate as Major Sheppard laid some cover fire. Soon after Ford saw Teyla and Rodney step through the event horizon, he turned around to look for Major Sheppard.

Sheppard was at a fair distance from the Stargate at that point. He stopped firing and was running towards the Gate, but the moment he saw Ford waiting for him; and being in possible danger he ordered him to go. Sheppard wasn't too far off and there was no way they could catch him on that short run towards safety.

Ford nodded and almost dived through the wormhole, rolling out on the other side. Where he waited with the rest of the team for Major Sheppard to step through the Stargate. But seconds passed by without a sign from Sheppard. After a few minutes the Stargate shut down leaving three team members in the dark about what had happened to their CO and why he hadn't made it back.

He should have returned at that very moment, maybe he would have been able to help Major Sheppard.

It was because of his inability to go back at that moment; Ford had a reason to be limping inside the room where the holding cell was. His leg was hurting him, but being a flesh wound Ford could stand the pain. He had no other choice.

The only change in the holding cell was that they had placed a small cot where Major Sheppard could sleep in.

As Ford walked in, the Major was still unconscious. He looked around and noticed they had placed cameras all around the cell to record his every word. Dr. Weir wanted to see every movement and every change the Major went through.

Ford moved closer towards Sgt. Stackhouse, who acknowledged his presence with a curt nod, "How he's doing?"

"Still unconscious, I think he was hit by 4 different stunners at the same time. He started moving a little in the last hour, that's all."

Ford glanced from Stackhouse to Major Sheppard. "Thanks Sergeant."

Ford moved around, circling the holding cell. His mind was half with him and half thinking of what to say when the Major would finally regain enough consciousness. As he circled the place for the second time, Ford stopped near the exit. He looked at Sheppard, who had his eyes open but they were glassy and empty. Ford sighed and walked out of the room, but before he could put one foot in the nearby transporter, he could hear Major Sheppard scream.

Ignoring the pain in his leg, Ford half ran and half limped back to the room, only to find John Sheppard screaming and trashing on the cot.

Sheppard arched his back upward and gasped. Then he slammed back to the cot, snapped open his eyes and frantically started to stand up. He fell on the floor and shouted while getting back to his feet, "Kolya, I'm gonna fucking kill you!" Panting he looked around and locked eyes with Ford.

Sheppard's brow furrowed, "Ford?"

Not sure of what to say the Lieutenant stared at Sheppard skeptically, "Major?"

Sheppard grabbed his head in his hands and sat on the floor. Ford stared at the Major, waiting for another reaction hoping that what he had just witnessed was true.

But when Sheppard opened his eyes again, he was definitely back in his Ignatius persona. "What do you want?"

Ford didn't dare to say a thing; the possibility of being able to talk with his friend was still in his mind.

Ignatius stood up and started walking around in his cell. He stopped and turned his head, looking right at Lt. Ford, giving him a cruel smirk, "How's the leg?"

Ford shifted a little uncomfortably and then replied with as much sarcasm as he could muster that moment, "I'll live."

Ignatius returned to his pacing back and forth, "Too bad."

Ford moved closer to the cell, "You had the opportunity to kill me. Why didn't you? Why didn't you blow my brains out?"

Ignatius turned and sat on the cot, "My mind was elsewhere. I wanted to get home before dinner."

"You are home."

Ignatius fell silent, while Ford had expected him to retort something nasty about Atlantis being his home but it never came. He seemed lost inside his own mind and Ford decided for the best to leave him alone for now. He quickly retrieved the video that had recorded the strange behavior and left to show what had just happened to Dr. Heighmeyer, Dr. Beckett and a hopefully conscious Dr. Weir. Who would probably want to see this too.


	5. Points of Authority

**Points of Authority**

Ignatius couldn't understand what had just happened. He had woken up, to find his mind filled with images. Memories he wasn't even sure were his, they were memories that gave him pain.

Pain that he didn't remember but felt to be his own, still he felt them close to mind like dreaming awake.

He couldn't explain it; Ignatius knew he was on a cell in the city of Atlantis. But his mind acted as if he was somewhere else, taking over completely.

He felt people around him, but he couldn't see. There was something covering his face, and some sort of recording on his ears. He was lying flat on a table, wrists and ankles tied. He felt incredible tired, but at the same time he was trying to ignore his surroundings. Ignatius was tired of hearing the recording, which was playing over and over again the same words. At the time he didn't care anymore about what it said, but he knew that it made him angry.

The recording stopped and heard a voice instead, "What is your name?"

He replied, name, rank and serial number. That must have been a wrong answer because in an instant he felt his body spasm out of control. There were certain spots that felt as if these people were stabbing him with knifes, very slowly.

Then it stopped and he heard the voice again, "Major Sheppard, you should stop resisting, one way or the other you will call yourself of the Genii."

He told the voice exactly where the Genii people could go. Not nice, they didn't respond too well to his outburst. He felt they loosened the restraints, but he was easily overcome. There were like five different people trying to control him. They took him off the table and carried him not far, where they placed him inside a tub. It was filled with ice-cold water.

His body was still tingling from the shock before, and the cold water made it worse. As he felt that every pore in his body was on fire, everything hurt. He felt his lungs fight against the cold that was making him feel as if he was suffocating. At some point, he didn't feel the cold anymore, only the pain, until they pushed his head under water, there he knew no more.

0-0-0-0

Yesterday had been truly a weird day for Elizabeth Weir. As she made her way to her office, she remembered how it had felt to wake up after being shot by a Wraith stunner. She had been released to her quarters after waking up, but still she felt like she hadn't slept in a week.

Elizabeth walked up the stairs when she heard Teyla's voice, "Dr. Weir! I must speak with you."

When Elizabeth turned to face the young Athosian woman, Lt. Ford appeared to their side carrying a laptop, "Dr. Weir, I have something to show you."

"Let's go to the briefing room," Elizabeth said quickly.

Just as they were about to enter the briefing room, Dr. Beckett appeared with Dr. Heightmeyer. Ford quickly informed Elizabeth he had called them up as he thought they might like to be kept in the loop about Major Sheppard's behavior.

Once everyone was settled in their chairs, Ford handed Elizabeth the laptop. She stared at it for a moment, while Ford started, "There is something weird going on with Major Sheppard."

Elizabeth's brow furrowed, "Weird?" As if things couldn't get any weirder, she thought, "He's already acting weird."

"No, I mean weirder," Ford stood up and walked to Elizabeth's side. He opened up the laptop, and set it up, "I need you to watch something.'

Elizabeth's attention turned to the laptop in front of her, as the screen came alive, Elizabeth could see John inside the cell, lying asleep in the cot. Then she noticed that John's eyes were open. She heard Ford's voice in the background talking to the sergeant, "Thanks Sergeant."

Seconds later John started to shake and trash around, then he screamed before finally waking up. After John screamed the threat to an invisible Kolya; Elizabeth saw what Lt. Ford meant by acting weird. For a brief moment, John seemed to be himself and not Ignatius.

Elizabeth realized that her mouth was hanging open and closed it quickly. "What just happened?"

Elizabeth stared at Carson expecting a full answer, but it was Teyla who answered instead, "You should see the other recording."

Elizabeth looked back at the computer and found the other recording Ford had prepared for her to see. This recording was from a different angle; John was in plain view, while Teyla could be seen in the background. John was lying on his cot, his eyes wide open. Teyla's voice could be heard, "I wish we could do more for you, Major."

Then John broke the silence, his voice was nothing more than a whisper, "I am from the Genii."

His face was blank, it didn't have the facial expression he had every time he said he was Ignatius. John looked to be in some sort of trance while he continued, "My name is Ignatius of the Genii… I am from the Genii… My name is…"

John stuttered for a moment, he sat on the cot and his face looked as if he was staring at an invisible person, "Kolya, you will regret this!" Then John gasped and fell back on the cot. Teyla moved closer to the cell, "Major!"

John stopped moving, he was now shaking, and when he opened his eyes they looked straight at Teyla, "Teyla… Is cold… too cold. Please tell them to stop."

"Who? What is too cold?"

Pain was spread across John's features, "It hurts…so much."

"What are they doing to you?"

John grabbed his head and started to breathe faster, and then he started to pull his hair. He stopped and then he looked at Teyla, "Teyla, kill them. Help me get out of here."

"Who do you want me to kill, Major?" Teyla asked trying to remain calm.

"The Genii, Kolya, every single one of them," John grabbed his head again, his face was screwed in pain, his eyes opened up again, and he stared at Teyla, "Why are you here? Came to remind me how good I was?"

Teyla seemed to conserve her calm, after a couple of seconds of silence she replied, "I came to help you realize that you are not of the Genii. That you are Major John Sheppard."

Ignatius chuckled, "You are so naïve; I came to this place and made you all believe I was one of your own. I have always been a spy."

Teyla moved closer to the cell, "I took your people to the Genii world. You were here before that. You have killed Genii soldiers during the big storm. How do you explain that?"

Ignatius stood up and started pacing around the cell, "I had to protect my cover."

"You are the one who is naïve… Ignatius; in your insistence to make us believe that you are part of the Genii."

Ignatius increased his pacing, clearly upset now, "I don't want to speak anymore, and I don't want to see anyone else trying to talk about me and my life on Earth. If you want to make me talk, get Elizabeth Weir, I won't speak to anyone else."

The video stopped and Elizabeth was too flabbergasted to speak for a minute, nothing coming to her mind anyway.

For a moment no one spoke and silence ruled the room. Eventually Elizabeth decided to clear her confusion, "He's acting like himself sometimes, how is that possible?"

Now it was Dr. Heighmeyer's time to talk, "From what I've seen, his mind is falling in some sort of trance. There, his subconscious seems to take over and he is able to be himself, the only thing is that Major Sheppard doesn't seem to be aware enough to understand what is going on."

Elizabeth was still confused, "He looked as if he has a split personality, and doesn't that make it all worse?"

"From what I was able to recognize, it looks like they used some tactics of Coercive Persuasion. They could have extended audio drills in which they made the Major listen to some sort of recording until he no longer rejected it, but believed it to be true."

Elizabeth stared at Kate, "Do you think that's how they turned him?"

Kate slowly shook her head, "No. It takes much more than that to turn a person, but the tactics they used could have included restriction of food and sleep. That could weaken the mind and use that to their advantage. Using certain punishments if he didn't react the way they wanted him to."

Now Carson interrupted, "And knowing Major Sheppard, he may have suffered hell before giving into their tactics."

Elizabeth's confusion only grew further instead of disappearing, "But that still doesn't explain why he's behaving like this now."

Carson shifted in his seat, "I'm not sure but I think that was developed after arriving here."

Ford stared at the doctor, "What do you mean?"

Carson continued, "He wasn't acting like that while he was in the infirmary. Maybe it's being here or that he's breaking from the brainwash. The brainwashing techniques they used are from another planet and maybe don't have a permanent effect or this is happening because he was stunned by four different stunners at the same time. It could be a combination of everything. Who knows? But after he tried to escape, something snapped."

Ford now turned to Weir, "I agree. But I think there was something in his subconscious the whole time."

Teyla stared at Ford, "I do not understand."

Ford took a moment to look at the group, and then replied. "Ever since he got here, he's been saying that he will kill us all. But when the moment appeared and he had the big chance of hurting us big time, he only did some minor damage. Yesterday he could have killed everyone in the infirmary. Why the threat to kill us while when the opportunity arrives he does nothing to really make it happen?"

Elizabeth closed the laptop in front of her and looked at everyone in the briefing room, "I agree. He wants to speak with me. Fine, I'll be there. If anyone detects some other change in his behavior, let me know," Elizabeth turned to Carson, "What about Rodney? How is he doing?"

"Fine, maybe I'll discharge him to his quarters tomorrow."

Elizabeth smiled, "Good. You're dismissed."

The group got up and Elizabeth watched them walk away from the room. There she wondered if she really was up to the task to confront the new Sheppard. Yes... and if that meant she had to treat him as a threat then so be it. She would do anything in her power to make him return to normal. If not, then Ignatius would have a long life behind bars.


	6. Wait and Bleed

**Wait and Bleed**

The cell had now become his home. Ignatius passed the time trying to think of ways he could escape from this wretched cell. But he mostly came up with nothing, while his mind was acting up and he felt like dreaming awake.

The memories of those dreams overtook him every time. He wondered why, if those were dreams then why did his subconscious give it so much importance.

The memories were deeply bothering him, by now he was filled with them again. The cell around him changed, he was still in a cell, but a different one. He remembered seeing it before, this time he wasn't on a table, but sitting on the floor with chains around his wrists. He looked around and noticed that his clothes had been removed. Somehow he felt weak, but still very angry. Someone was standing in the shadows and that someone was talking to him. The voice seemed familiar and yet he couldn't place it.

"You will give up eventually."

Words came out of his mouth, "I will keep with my end of our deal, and don't you ever doubt it."

Anger was now raging inside him, the person in the shadows let out a soft chuckle, "Major Sheppard, you can threat me all you want. But in the end you will call me master."

He couldn't understand it, the voice was so familiar. Then instead of retorting another threat, he flipped his middle finger and stared at the person, "Fuck you, Kolya."

Kolya... Commander Kolya walked closer to the light. His Commander Kolya... then he reacted... _'He called me Major Sheppard'_

Kolya closed in, took out a small gun and shot him a dart in the chest. He remembered the dizziness, the blackness.

Someone called his name, "Ignatius"

He blinked; Elizabeth Weir was outside his cell. He thought again of his last memory, _'Memory? Is it a memory? Did the Commander torture me?'_

In his mind he tried to come up with excuses of why he had just dreamed or remembered Commander Kolya torturing him. Maybe he had fallen so deep into the Sheppard cover that his people had to snap it off of him... maybe. Still he felt of the Genii, there was no doubt about that.

He blinked again, while Elizabeth Weir was still staring at him. Finally she decided to formally talk. But then something completely unexpected happened, she ordered the cell to be opened. Ignatius looked at his surroundings; the room was full of soldiers, even the ones he had wounded days before. There was no way he could do something... but still, a good scare wouldn't hurt anyone. He smirked, while staying still on his cot. He would wait for the opportune moment.

-0-0-0-

When Elizabeth walked into the room, Major Sheppard was in the same sort of trance that she had seen him previously in on the videos. She called his name twice but he didn't respond. She thought of their last encounters, first their meeting at the infirmary, and then he stunned her and tried to take her to the Genii.

Ever since then she had tried to block that incident from her mind, because if he had succeeded, she would have been in a lot of trouble. Right there, she wished for a miracle, something that would make it all better without anyone having to suffer no more.

Elizabeth was now staring at Ignatius, while there was still no response. She decided to do something risky, which could actually give them some trust between them. She ordered Lt. Ford to open the cell. The action itself seemed to take Ignatius by surprise, which she knew he wasn't expecting that from her since he had attacked her earlier. She walked in with a formal hello.

He stared at her, while Elizabeth tried hard to ignore the menacing stare he was giving her, "You wanted to talk to me?"

Ignatius stayed seated, "You have to let me go."

Elizabeth felt her face tighten, "We have talked about this. You wanted to talk so here I am," she noticed that he was evading her eyes now, so she decided to press on. "There are things I would like to know."

Ignatius was now staring at the floor, "I won't tell you anything, I won't betray my people."

That was the answer Elizabeth had been expecting to hear, "I'm not interested in knowing about the Genii. I already know about them. It's you I want to know about."

Ignatius smiled sarcastically, "Came to remind me how good I was? About my life here? About being John Sheppard?"

"No, I want to know about you. I want to learn more about Ignatius."

Ignatius fell silent and looked up at her at once, staring in disbelief. "Still, I won't tell you anything."

Elizabeth gave him a questioning look, "Really? I just wanted to know how you were raised to the professional spy that you are. After all, you did manage to fool us all. We truly believed you were from Earth and one of our own."

Elizabeth was finally getting his attention and with that came sort of a victorious feeling. "In fact... I'm curious about how you know so much about Earth," Elizabeth noticed Ignatius' face fill with smugness, "I did my research."

Now it was Elizabeth's turn to stare at Ignatius with a surprised look, "Research? Err... mm-hmm... Okay, let's move on. I imagine you were raised by your parents and when the time came you joined the Genii military. Served your time well and was chosen to become a spy for the Genii, which must be an honor. You did your research and then you were given the assignment to infiltrate the city of Atlantis."

Ignatius gave her a small nod, Elizabeth knew this was the moment she was waiting for, "Good, then I'm sure you can explain to me how you managed to be on Earth. How is it possible that I can clearly remember the first time we met in Antarctica, where you were stationed at McMurdoch's? We met in an underground room where you were discovering the universe in an Ancient chair."

Elizabeth felt a little bit more confident when she saw that Ignatius' face changed into confusion, which made her decision to press on easier, "How you explain that, I wonder?"

Ignatius face remained confused, while he was frantically looking around. He was most definitely searching his mind, trying to come up with an answer, "I... made you believe it. You are weak, how much more can you expect from a woman?"

That wasn't the sort of reaction Elizabeth was hoping for but she didn't let her focus down for it. She decided to try a slightly different approach, "How could you, John? I thought you were stronger than that. How can you call yourself of the Genii when you killed more than sixty Genii soldiers when that big storm was going to hit the City?"

Ignatius was still looking, less frantically though, around his cell, "I knew you were going to bring that up."

"Then you remember?"

"I was protecting my cover. So, you see Elizabeth, no matter what you say, nothing will change the fact that I am one of the Genii, and that in the end I will give Commander Kolya the key to Atlantis. I will give him you. I will sit and watch how the Genii take control of the City."

Elizabeth felt a bit shocked at the hatred in his words, "We won't allow it and you know it."

Ignatius ignored her and continued, "I will reclaim my place right beside Commander Kolya. Maybe he will give me the honor to execute every single member of this expedition. The lesser important will go first, they won't suffer much. I think decapitation will be enough, but for the important ones it won't be that easy. I will torture them until their last breath," Ignatius gave Elizabeth one nasty smile before continuing. "Then of course ... you. You are quite a beautiful woman Elizabeth; you will make the Commander very happy. In fact I wish I could be there, when he's breaking you... when he makes you his. I wish I could be there the moment your soul is destroyed."

Elizabeth was beyond shocked. She closed in on Ignatius and slapped him in the face, "The John Sheppard I know would never have said that."

His face filled with pure rage, he hadn't expected that kind of reaction from her. Slowly he moved his glare until he locked eyes with her. Suddenly and without any kind of warning he grabbed her chin and held her so tight his nails were digging into her skin. The reaction of the guards was quick. In less than five seconds he had five stunners and two guns pointed at him. He looked at the soldiers, then back at Elizabeth, "Then I can't be John Sheppard, can I?"

Ignatius let go of Elizabeth so harshly that she staggered on her feet. She took a moment to control herself. His outburst was doing no good to her self-control of her emotions. She had never seen so much hatred in anyone. And for the first time she really believed that John would hurt them if he had the chance.

Elizabeth was trying to control the knot anger and shock were forming in her chest, which only made it worse and brought her to a point where she started hyperventilating. She was trying with all her might to control herself, but Elizabeth knew that she was not going to be able to continue with the conversation. So she did the only thing her body allowed her to do, turn around and storm out of the room.

Ford, who had witnessed the event, saw Dr. Weir walk out. He ordered the cell to be closed, but when he looked back at Ignatius he was smiling and waving his hand while saying, "Bye."


	7. Whisper

**Whisper**

Elizabeth stormed out of the room, feeling the stress, worry and frustrations of the past couple of days building up in her chest. The knot in her chest had now moved to her throat, and it hurt. She placed her face on her hands and breathed deeply.

Lt. Ford had walked out after her and found her standing against the wall, "Dr. Weir, you ok?"

Elizabeth quickly stood up straight and forced her mind and body to calm down, "I'm fine, thank you."

Then she turned around and walked to the nearest transporter, but instead of going back to work, she headed to her private spot. The balcony, that was hers and hers alone, was situated across from her room.

She needed some alone time as she could feel her mind wasn't going to hold on for much longer and she didn't feel like breaking down in front of everybody. She couldn't be seen like this, she was a leader after all.

Once at the balcony, she opened the door and was immediately engulfed in a cool ocean breeze, which felt as if it were taking all her worries away. Elizabeth made it to the railing, placed her arms on top of the railing and her face on her hands.

Every ounce of stress, worry and frustration wanted to get out from her system, and yet she couldn't. She couldn't let this situation take control over her. At least that is what she wanted to think.

-0-0-0-0-0-

Rodney smiled widely, being released from the infirmary at last had boost his energy a little. He was still feeling some pain, but Carson had provided him with some painkillers and had ordered him to take it easy for the time being.

Carson had threatened Rodney that if he wasn't in his quarters when he checked by, he would immediately confine Rodney back to the infirmary for a few more days.

Rodney slowly made his way back to his room when he noticed Elizabeth walk out of a transporter heading onto the balcony across from her room. Rodney stopped, noticing she looked as if she was about to fall apart.

He moved towards the door of the balcony as well but hesitated to go out; as he wasn't sure he should intrude on her privacy. But then again maybe she needed someone to talk to. Rodney hesitated some more, feeling kind of awkward but after a while he could no longer resist the feeling to go in and lend his shoulder to her. There was no way in hell he was going to let her carry this burden, or whatever it was, alone.

He opened the balcony door and slowly made his way outside. He found Elizabeth sitting on the balcony floor against a wall. Her eyes were focused somewhere on the floor beneath her.

Elizabeth looked up, and when she realized that it was Rodney the person in front of her, she quickly stood up, "Aren't you supposed to be in the infirmary?"

Rodney gave her a small smile, "Carson just released me."

"How are you feeling?"

"Given the circumstances… I'm great!"

Elizabeth nodded and fell silent. The silence hung around for a moment until Rodney said, "I was going to ask you the same."

"Huh?" Elizabeth let out, with a frown on her face.

"How are you doing?"

She took a deep breath, soothing her troubled mind, "I'm fine."

"You don't look fine," Rodney was far from satisfied with her answer as he could clearly see she was far from fine. She was troubled and damn him if he wouldn't find out what it was.

She sighed heavily, "It's just this... John... the Genii."

"What happened?" Rodney asked.

Elizabeth shifted uncomfortably while she stared at the ocean. Realizing Rodney was going to let go, she told him what had just occurred while visiting John/Ignatius.

Rodney listened without interruption and what he heard wasn't all that good. He waited in silence until she was finished but by then Elizabeth was trying hard to control the anger in her voice.

"I'm sorry. I feel so stupid, I went in there believing that at least we were going to gain some hope. But there we have a Major Sheppard who just told me that he wants to watch when Kolya rapes me... I don't know if I should be frustrated, sad or really, really angry."

Rodney stared at Elizabeth in silence. He had never been good at this comforting-thing and as a result he never knew what to say or do in this kind of situation. Elizabeth leaned completely against the railing and looked down, "I feel so stupid."

"Don't... I just can't believe he said that." Rodney watched her and realized that anger was starting to build up on top of what anger he had been feeling from being shot by the captured Major. He wasn't angry with the Major, he could never be angry with that man or at least not for a very long time.

But this wasn't the real Major Sheppard; this was a man claiming to be someone he was not and therefore in no control of his actions.

No, his anger was directed at the Genii, the people whom had tried to take their technology by force. Attempting to take Atlantis, and in the process threatening the lives of everyone on the base. _Haven't they done enough? What the hell do they want from us?_

Rodney kept Elizabeth some company, talking about everything and nothing, allowing their minds to be on other matters. After a while Rodney knew Elizabeth had calmed down to an acceptable level and talked her into taking some rest. He was sure that after a good nap she would be able to see things more clear and maybe deal with the rest of the people in Atlantis.

Elizabeth agreed without complain and Rodney made sure she actually entered her room and crawled into her bed. He hadn't yet turned back to the door or she had already drifted off, exhausted by all the emotions and events.

Knowing Carson would be checking on him in his quarters he headed out that way but at the transporter he changed his mind and decided to confront the son of a bitch that had shot him. He would have the bastard tell him everything they needed to know. And he had absolutely no intention to leave Ignatius before he had at least the minimum chance that Major Sheppard was still there.

But first he would say what he had to say, he would make it his job to let Ignatius know what they thought of him. It might be helpful afterwards.


	8. Freak on a Leash

**Freak on a Leash**

Rodney's body protested dearly, but he chose to ignore it. He was feeling angry, angry at the whole ordeal the Genii had caused. He was on his way down to have a serious talk with someone who used to care about them, which this same person lacked very much at this very moment.

McKay's mind wandered, he wanted to help so badly, even though he had no idea if having a conversation with Sheppard, at his present state, would do much good. Rodney stopped at the door, popping his head inside. He saw the major pacing back and forth inside the small cell.

Rodney took a quick moment to have a better look at Sheppard. He was wearing white hospital scrubs and while the hair was still messed up, it wasn't as before. And from Rodney's point of view, the beard didn't suit John at all.

Ford had been talking to Sgt. Stackhouse, when he noticed Rodney walking in. The young Lieutenant threw the scientist a large smile, "Dr. McKay... Good to see you! How are you feeling?"

Rodney glanced back at Ford, "I'm fine, thank you. Carson just released me. I thought I'd come down here and give it a try."

Rodney didn't need to explain to Ford what he meant by it. As the Lieutenant knew well enough he was going to have a little chit-chat with the man now known as Ignatius. "Has he said anything after Dr. Weir left?"

Ford turned grim, "No, but he has become more agitated, though."

Rodney moved closer to the cell and immediately Ignatius stopped his pacing.

"Feeling well?" Ignatius asked with a smirk on his face.

Rodney stared back, his face showing no emotions at all, "Fine... not thanks to you."

A heavy silence hung in the air as the two kept staring at each other, trying hard to make the other look away or break the stare in any other way. Finally Ignatius broke the stare and walked towards his cot. "Came to pay respects and try to convert me?"

"No, I came to call you a coward."

Ignatius seemed to freeze on the spot, showing his back to Rodney, "I am not a coward."

Rodney stayed still, his body tense, "After what you said to Dr. Weir, I can call you a coward. In fact, I don't know who is more a coward, you or your dear Commander Kolya," Rodney gave him a thoughtful look, one that certainly didn't miss its effect.

Ignatius turned around, his face filled with anger, "Don't you dare say his name!"

"I can say it, and I can curse it. I curse the moment he knew of our existence,"

Ignatius was clearly trying to keep his anger controlled and decided to keep quiet, allowing Rodney to continue, "But that's not why I am here."

Ignatius relaxed a bit but kept staring, "Then to what do I owe your presence?"

"I came to talk to John."

Ignatius laughed derisively, "Bad luck... you just missed him."

Rodney tried to ignore the attitude Ignatius was giving him and continued, "I know he's here somewhere. I don't really care if he doesn't answer me. Just wanna talk."

Ignatius relaxed completely now and laid down on his cot, "Knock yourself out."

Rodney started pacing, circling the cell, "First of all... I'm sorry, Sheppard. I'm sorry we left you behind," Rodney stole a glance at Ignatius, who was clearly ignoring him. So he continued, "Secondly, we will not allow you to harm anyone."

"There are things you cannot control." Ignatius cut Rodney off.

Rodney ignored the comment and continued, "Thirdly, if we are not successful in removing this coward persona you seem to be now..." Ignatius got up so fast, which gave it the impression he had just burned his bottom, and presented Rodney with a murderous glare while the scientist calmly continued, "...We won't allow him to go free. And finally, if we ever grab that bastard Kolya, I swear to you I will personally fulfill your end of the deal."

Ignatius frowned, "Deal? What deal?"

"I will kill him, Sheppard. If is not me, I know a few people who won't mind doing this for you... I promise." Rodney noticed how Ignatius suddenly went from furiously calm to extremely strange.

Ignatius walked towards Rodney, causing him to back away a little from where he was standing near the bars. "What deal! Whose deal!"

Standing at a relatively safe distance Rodney frowned, "I thought you didn't want us to tell you who you're supposed to be. The things you have done. But in my humble opinion I don't think it'll be bad for you to know... to remember."

Ignatius' behavior changed once again. He looked agitated almost desperate, "What? Know what?"

Rodney eyed Ignatius suspiciously, but answered the question dutifully, "Our last encounter with the Genii, you made a deal with Kolya that the next time he played nasty you were going to kill him. I'd say that this qualifies as a nasty move."

As a bullet to the head, Rodney's last comment sparked something inside Ignatius. Something he couldn't explain, he remembered his dream in which Kolya called him John Sheppard. And he had talked about a deal ... a deal with Kolya. He shook his head, "No, it cannot be... I am Ignatius of the Genii, my people are the Genii!"

Seeing Ignatius' reaction, Rodney continued knowing he was making the other one doubt himself now more than ever, "What? You remember?"

Rodney stared at the man inside the cell; Ignatius' face was filled with confusion. Rodney could also see a glimmer of hope in the confused man's face, "You know! You can see it in your mind! I bet you are beginning to question..."

Ignatius cut him off with a soft but desperate, "Shut up!"

Rodney cheered inwardly. He had won his first battle and was pleased to see his opponent failing in his attempt to remain untouched by what he was saying. "You do! You are questioning yourself!"

Ignatius started pacing frantically back and forth, "Leave me! LEAVE!" His plea was more desperate than he had intended to, but Rodney didn't feel like leaving or giving up just yet. He knew Ignatius was letting his guard and about time too, "Tell me John, how it felt to shoot Kolya?"

Ignatius lost it. _'Shoot Kolya? The man is insane!'_ He looked up, straight in Rodney's eyes, and screamed, "Shut up and go away! Just go away!"

But Rodney kept pushing, "Why did you let them, Sheppard? Why did you allow this to happen?" Rodney knew that this wasn't John's fault, but he had seen something in the eyes of the man that called himself, Ignatius. Recognition? Confusion? He didn't know but he knew he could use it to lure John's conscious to the surface.

In an act of rage or maybe helplessness, Ignatius started hitting the cell's shield, "Fuck you! Go away! Leave me alone!"

Rodney closed the distance he had stepped back when Ignatius had first started to advance in his direction, and replied equally as angry, "Don't want me here? Then you should have aimed a little better," Then he saw how Ignatius raged and screamed in anger, "I am from the Genii, my name is Ignatius of the Genii!"

Rodney tried to remain calm, "You can scream all you like, but that show will never convince me that you are not John Sheppard!"

Ignatius covered his ears, like he was a child would when it hears something it doesn't like. In his mind Ignatius started to see images, memories, dreams, people, and places all at once. Voices too, but the voices were mixed with the constant reminder that he was of the Genii. For once he felt as if he was really going crazy. For a moment he saw all the people that had him in the cell, not like his captors but like his friends.

Friends... from a distant dream he had long ago. He needed to get out; he needed that man outside the cell to leave. He needed to think. But at the same time, Ignatius felt a knock in the back of his mind, which was trying to remind him that his subconscious was screaming for something. Like an animal fighting his way out of a cage.

Rodney had stayed completely still as he was watching Major Sheppard fighting with himself.

Ignatius stumbled, as he tried to get a grip of himself. He was aiming for his cot but instead he fell to the floor. There he pulled his knees to his chest, covered his ears with his hands and started rocking back and forth. He wanted it all to go away, he wanted everyone to disappear. He knew that somehow what he had just heard was not real. It couldn't be real because he was of the Genii.

Rodney stared at Sheppard; he really wanted to know if there was some hope for his friend.

Yes... friend. Maybe not at the beginning, but after all they went through, Rodney was confident in considering Major Sheppard a friend. And if tormenting his brainwashed mind was the way to get him back, Rodney could stay there the rest of the day.

But he felt his body protest, if Carson knew that he had been doing a lot of stuff he wasn't supposed to, there would be hell to pay. Deciding he wouldn't want to tell Carson why exactly he had crashed again, he decided for the best to give it a rest for now and find his comfy quarters to take some rest.

But the moment he turned to leave he could hear a faint, yet familiar whisper directed at him, "Rodney?"


	9. Crawlin

**Crawling**

Rodney turned around, expecting Ignatius to shout some threat or another, but instead he could witness how the man inside the cell started talking softly, more to himself than to the scientist, "Rodney... there's nothing to forgive."

Realizing what was happening, Rodney closed the distance between himself and the cell, "Sheppard?"

But John kept staring at the floor and talked as if Rodney hadn't said a word, "None of it is your fault. Too bad you're not here. But I just have to say it... even if it is only an illusion."

Rodney quickly picked up on his talking and replied, "No! Major Sheppard, this is not an illusion! You're back home, you're in Atlantis!"

The Major looked up, straight at McKay, "They want to turn me Rodney..." And with a pitiful sigh he added, "...and you're not really here."

Rodney noticed that Sheppard's expression was one of a broken man, "Major, look at me! You're in Atlantis."

He made sure to stress on every word so Sheppard would know he was telling the truth. But all the man did, was ignore him like he really wasn't there but just a figment of the broken man's mind.

"I have tried, I'm still trying... I don't know how much longer my mind will hold. I don't want to give up."

"Then don't! You can come back. Just don't give up!"

"It really is a pity you aren't really here."

In some way Rodney felt kind of flattered Major Sheppard would picture him in a time of so much need. He thought that he was nothing more than a true pain-in-the-Major's-ass, who could do not much right just because he was a scientist.

Sometimes Sheppard would remind him of General O'Neill, but now he realized he wasn't just the geek on the team, he was a friend whose sixes would be covered in times of danger. And Rodney would definitely do the same, even if he considered himself not one of the bravest men on the expedition-team.

Rodney noticed the way Sheppard acted, he had returned to his silent and catatonic self, his gaze fixed on a non-existing point somewhere on the opposite wall. McKay decided it would be best to call it a day and leave the man to rest. He quickly excused himself and left the holding room.

-0-0-0-0-0-0-

This whole situation he found himself in was far too quickly turning into an unending nightmare, in which he didn't even know who he was or if in fact he was the same person. John had somehow awoken to find that Kolya was playing twisted games with him and more so with his mind. He had woken up to see Rodney trying to question him. _That is a nice way to dig out information; at least I said what I wanted to say. _

For a brief moment he had seen himself in Atlantis, home. He was in the same cell they had used to keep their first captured Wraith, who he affectionately had named Steve. But he didn't care; none of it was real after all.

Not Ford or Teyla, not even that realistic version of Rodney. He couldn't deny however that seeing the scientist had sparked a memory inside his mind. It was a dream he had, in which he had wanted to kill Rodney, but he couldn't for the life of it remember whether he had been successful or not.

The more he glanced around his cell, the more he wished it was real. The more he looked at it, the more he wanted to believe. But ever since Kolya had changed his tactics, there was no way he was going to help that bastard hurting the people he cared about.

In an instant he knew what he had to do. He promised himself he would try everything in his might to break free, or just die trying anyway. If he were to die, he didn't care. All he wanted was just to be free. He wanted to be able to relax and to not think about all the nightmares that haunted him every time he dared to close his eyes.

-0-0-0-0-0-0-0-0-0

Elizabeth was sitting on the edge of her bed, debating whether she was going to go to her office or not. She was feeling so tired, having slept very little the night before. And most importantly she didn't feel like discussing with anyone what had happened with John in his cell the day before.

He had spoken so harshly, so angry and with so much hatred... Elizabeth honestly didn't know if she was going to be able to talk with him again, in a civilized way anyway. But if there was no other option, she would do it. John was like family, just like the rest of the people in the city, and one does his very best when it comes to family or best friends.

But at this point, Elizabeth didn't know what to do since John wasn't responding to them. They didn't even know how to treat him. It was just a waiting game.

Deciding for the best to move, she shuffled towards the mirror and almost jumped back at what she saw. Elizabeth stared at her reflection where she could clearly see the marks John's nails had left. She quickly made a mental note to evade Carson Beckett as best as possible, in fact she would be happy if she could be completely invisible the rest of the day and not have to worry about anything.

With that thought in mind she walked to her door and opened it up to start her day in the city. She absentmindedly walked out and almost bumped into Lt. Ford, who looked exactly like how she was feeling, "Dr. Weir, I was looking for you."

Elizabeth frowned, "What's wrong?"

"We want to go to the Genii home world,"

Weir did a double take and had to suppress a hysterical giggle. Had her crew gone mad? "W-what?"

Ford didn't waver, "**We** go there, and demand to know what they have done to the Major."

It then hit Elizabeth like a ton of bricks. All the young Lieutenant wanted was his CO and friend back as he was before, "I don't think that is such a good idea."

Ford opened his mouth to say something harsh no doubt, but at the last minute changed his mind and went with, "We need to do something for him, and we can't just leave him locked up forever."

"I understand Lieutenant, but what guarantee can you give me that the moment you set foot on their planet they won't take you and your team and do the same thing they did to him, or worse kill you on sight. They have no need for question, Lieutenant."

Now it was Elizabeth's turn to look stern, "I know that you want him back, but until you give me something more to work with, I'm not sending you anywhere in some false hope that it'll bring John back."

Ford felt like begging, "What are we supposed to do then? Talking no longer works since Doctor McKay made it worse yesterday. Not even Ignatius responds."

Elizabeth frowned, "Rodney did what? When?"

"Yesterday afternoon. It got really heated. Major Sheppard talked like himself for a bit..."

"What did he say?" Elizabeth cut him short.

"Nothing much, I don't even think he is aware of his surroundings."

Elizabeth was about to ask something else, when Carson appeared in the hallway. "Elizabeth, can I talk to you?"

Weir cringed, remembering her mental note. She glanced from Ford to Beckett and was about to respond to Carson when Ford started talking before her, "I should be going back to the holding room."

"Let me know if anything changes!"

Ford nodded and walked away.

"What can I do for you, Doctor?" Elizabeth asked sounding a lot more cheerful than she had intended to but she couldn't care much about it at the moment.

Carson's gaze immediately locked onto her face and he grabbed her chin to have a closer look at the scratches, "Major Sheppard did this?"

Elizabeth tried to break free from his grasp but he gave her his best Doctor-look. "You should have come to see me immediately instead of today."

She tried to dismiss the issue and shrugged, "It's nothing. I'll live."

Carson shook his head and gave Elizabeth a knowing look, "I talked to Rodney dear. Come on, walk with me!" Beckett left no room for argumentation and pulled the leader of Atlantis with him.

"I need to go to my office, Carson. Can we do this some other time?"

"Humor me."

Elizabeth sighed and decided for the best to follow Carson's lead.

Once in the infirmary Beckett ordered her to sit on one of the few chairs and to stay put. He took his time to treat the minor injuries, disinfecting them and applying a bit of antibiotic cream. The moment he was finished with his job, he took another chair and placed himself opposite Elizabeth, who hadn't yet said a word or had even winced when he knew he was touching a particular soar spot. "Well, I don't think it'll kill you. But next time I'd like you to come to me when it has happened, not the day after."

Elizabeth gave Carson a small smile, "It's good to know that some people still have their sense of humor."

"Somebody has to, with all that is happening around here."

Elizabeth knew she wasn't going to get away with a simple 'you'll live', she could feel his questions bubbling to the surface and quickly tried to change to subject away from her. "How's Rodney?"

Carson crossed his arms over his chest, "He's ok. He did some unauthorized things, but Rodney is a strong lad. He told me what happened between you and Major Sheppard."

Elizabeth nodded but said nothing. Carson decided to continue, "Do you want to talk about it?"

Elizabeth tried to dismiss him again and slowly shook her head, but seemed to change her mind at the very last minute or so Carson thought. "There's nothing to say really."

"Well, from what I heard, he saved the worst for you."

Elizabeth stared at the doctor and replied, "And what do I say to that, what do I do?"

Carson opened his mouth to say something but was interrupted when the infirmary doors opened and Dr. Heighmeyer came walking in. When she noticed Carson and Elizabeth, she smiled and moved into their direction, "It's good to see you both together. I need to talk to both of you about something."

Elizabeth looked at the resident psychologist and saw lines of worry edge around her eyes, "What's wrong?"

"I just saw the tape from yesterday and I think Major Sheppard has made some progress. When Rodney talked to him, he said some harsh things to Major Sheppard, and it surprisingly had a strong enough effect to make the Major surface again."

"How long?" Carson had a basic understanding of Heightmeyer's job and knew that progress was good. Even though the man had still a long way to go before returning to normal.

"Just a couple of minutes, but definitely longer. But from what I saw on the tape, Major Sheppard doesn't seem to grasp he's already turned. He spoke as if he was still undergoing the brainwashing. He believed Rodney to be nothing more than a figment of his imagination. He thought he was hallucinating."

Elizabeth frowned and felt anger rising in her chest. Why was she saying all those things, while she hadn't even took the time to go down there and see him face to face. "Have you talked to him yet?" The question had sounded more aggressive than Elizabeth had intended, but she didn't care.

Kate did noticed Dr. Weir's sudden change and answered calmly, "I will soon. For now he's not a threat to us but if something happens, I recommend the use of a stunner but only when it's absolutely necessary."

Elizabeth was confused, "Why?"

"I believe it was the stunner that started causing the separation of the personalities. If we use it again and again, I don't know if it'll make him improve and become John Sheppard or sink entirely into his Ignatius persona and make the damage worse."

Carson got up but stayed near his chair, "Can we do something for him?"

Kate's face turned grim, "I'm not sure; we should keep visiting and talking to him. But as you know, Ignatius is aware that we are talking to him as John. And judging by what I have seen on the tapes, he really doesn't like that. I'll be going by the holding room either tomorrow or the day after tomorrow. I believe that even as Ignatius, he has to have John's memories and thoughts. So I'm going to use that to my advantage."

Elizabeth really hoped that they would very soon find a way to help John, because if they didn't then she would have to make the most difficult decision she had yet to make ... she would have to decide John's fate and future, something she really didn't want to do.


	10. One Step Closer

**One Step Closer**

There was not a single shred of doubt in his mind that commander Kolya had tortured him. After blacking out a couple of days ago, Ignatius was feeling awkward. Sitting on his cot, he knew that there were more memories surfacing and he had no idea what to make of them.

In each and every one of them he saw himself as John Sheppard and each time it felt as if he was reaching for something and yet every time he would come up short. The one now floating through his mind intrigued him. Even with all the doubts present, Ignatius felt like he was still of the Genii and that there must have been a mistake.

What had happened while he had blacked out? He had absolutely no idea and yet at the same time it felt strange. It had never lasted so long before. These damned memories were invading his senses again. He was still in the same cell as before and still in pain, with Kolya smiling down on him. All he really wanted to do was to kick that smile off the man's face.

He looked around, finding he was sitting on the floor, resting his back against the wall behind him. Kolya was seated in a chair on the other side of the room, far out of his reach and the ever present smile, "I have a better idea Major, there's a process I have used in the past. It has been almost perfect, not all subjects are equally as strong. But I am pretty sure that by the time we're done you will call yourself of the Genii. You will follow every command I give you and by the time this is over, you'll be dead and I'll have Atlantis." The evil laughter he had expected didn't come which was a small relieve.

"You'll never turn me!"

"That might be the case, Major, but first you do me some favors. Willingly."

"I don't think so."

Kolya had reached the end of his short amount of patience he had when he had the pleasure to torture a future Genii and got to make his way over to where John was sitting against the wall. "I don't care about what you think Major. Once you agree to work with us, you will bring Dr. Weir to me. She will be a compensation for all that you have done to us. And maybe ... something else too."

Anger shot through his veins, and in one sudden but rather fluent movement, Sheppard forced himself to get up and tried to hit Kolya. But instead he could only struggle against the unexpected hands that held him down, forcing him to kneel in front of Kolya like a slave to his master's feet.

Kolya approached and grabbed John's hair, pulling his head back and giving him his most nasty smile, "Worried about your Commander, Major Sheppard? Well... you should, because when you bring her to me, I will break her in so many ways that you won't be able to recognize her once I'm through with her."

What happened next happened so fast that he hadn't seen it coming if he had been able to. Kolya slammed his fist into John's face. The darkness that followed was expected and almost welcoming, but it gave more questions to Ignatius. Was he really a member of the Genii or was he in fact Major John Sheppard?

_No! Ignatius, Ignatius is my name. I am from the Genii. I am Ignatius of the Genii. _He repeated the words in his head as if it were a recording. It felt like a recording... a recording... _ Damn it!_ Now he was confused. There was something going on, he knew it for sure. There was something wrong with him, with his mind. It was weird how the anger didn't come from within but Ignatius himself felt like doing some major damage to Kolya.

The memories were becoming stronger and Ignatius could actually feel it, the pain was overcoming his senses as another memory took over. Blows, kicks and punches coming from everywhere. Then without reason they stopped and all he could was cough, feeling blood in his mouth. In between the pain he looked up and there he was, his commander, his torment.

He was barely able to breathe, he couldn't even sit up straight, but Kolya's shadow was hovering near. "Major Sheppard, either you tell me what I want to know or I will promise you that I will beat you within an inch of death, nurse you back to health and repeat the whole process again."

He kept silent; he wasn't going to give Kolya that pleasure.

_Wait! What pleasure?_ Kolya was supposed to be his commander, not his enemy. Something was happening; maybe these people were trying to confuse him into believing he wasn't of the Genii. Maybe they were the ones doing all this torturing. But if the dreams... the memories were true, it would mean that he was in fact Major John Sheppard.

No! That couldn't be. He was Ignatius of the Genii. They only wanted to confuse him. He knew that in order to clear up the anger building up inside of him, Ignatius had to return to the Genii home world.

He needed to get out of his cell but looking around Ignatius knew he would need a little outside help. It had to be night already, because there were only three soldiers outside the cell, not the usual five. A door opened and someone walked in, Ignatius recognized her as one of the doctors, Dr. Heightmeyer. She carried a notebook and placed a chair in front of the cell. "Good evening, Ignatius."

Ignatius looked at her with little to no interest, "Have they finally gave up and sent you instead?"

She didn't show him any emotion as she replied, "I have a job to do, and we need our ranking military officer back."

Ignatius stared at the doctor, "I see what you want, you want to turn me against my people. You want to confuse me so I'll tell you things."

Kate stared back, "What have we done to make you think that? We only want the real you back."

"John Sheppard was not real." Ignatius didn't really know, why he was insisting on convincing them he wasn't their Major while in his mind doubts were building. But he decided to play the game their way and maybe he would be able to take something from them.

Kate started to look through her notebook and took out a small piece of paper, "Let's review a few things here. You are Major John Sheppard, US Air Force. You are the son of Colonel James Sheppard, who is a decorated Cold War officer. You got stationed at Antarctica after disobeying a direct order from your superiors in a mission in Afghanistan. You possess the ancient gene and you were reported missing in action four months ago, after an ambush off-world."

Ignatius glared at her, "I already knew that."

Kate stared back; she really wanted to know how far into his new persona the man on the other side of the cell was. "I have a few questions."

"I won't answer them."

Kate wrote something in her notebook and looked up at Ignatius, "I'm not interrogating you, just a few simple questions. I just want you to answer the first thing that comes to mind."

Ignatius gave her a small smirk, and cocked his head to the side, "Right... the whole doctor thing."

Kate rolled her eyes, noticing the Major's humor had survived after all. She pushed the thought to the back of her mind and continued, "Where are you?"

Ignatius' brow furrowed, "What?"

"Just answer the question. Where are you?"

Ignatius sat straighter on his cot, "In a cell."

"Where is this cell?"

"Atlantis."

"Where were you born?"

"The Genii home world."

"Who is Steve?"

"A Wraith."

"What's a puddle jumper?"

"A small ship that fits through the gate, hence the name puddle jumper."

"Why did you leave your work at the SGC?"

"I never worked at the SGC."

Ignatius was feeling confused by the questions but the doctor didn't give him time to think. And she continued with more force or so it seemed. "Why did your father break with you?"

"He hated me after Afghanistan." The answer came so natural, that Ignatius had to blink for a second. He stopped and gave his answer a second thought, but she didn't give him time to really understand it all, she kept pushing, "What is your name?"

"Major John Sheppard, US Air Force." Ignatius couldn't believe he had just answered with the one name who claimed wasn't his.

Kate looked at him with interest and continued, "I thought you were Ignatius."

Ignatius got up and walked straight towards Kate, who couldn't deny she was feeling uncomfortable even though the man couldn't reach her. "What the hell are you doing?" He started pacing back and forth, "You want to turn me!"

Kate closed her notebook and got up as well, "No, I just wanted to show you that you might be wrong in believing that Ignatius is real. Just think about it, there must be holes in the story of your life, while John Sheppard's life is complete. You should understand that there is something wrong going on in your mind. I have seen you, you talk in your sleep, and you talk as John Sheppard not as Ignatius."

This was starting to feel more and more like when McKay had talked to him. Why did it affect him so much? He knew now why, they were trying to use him. "You are trying to confuse me, I am from the Genii."

"Then what happened two days ago? When Dr. McKay was here, I saw you talking to him as John Sheppard."

"No."

Kate shook her head a little and decided to change her tactics, "Do you dream?"

Ignatius felt the whole thing was absurd, "What's that have to do with this?"

"Just answer the question, do you dream?"

Ignatius was starting to loose his patience, "Why do you care what I dream about?"

"So, you dream. What happens in these dreams?"

Ignatius remained silent, but Kate pressed on, "Does Commander Kolya appears in them? Ignatius didn't answer, feeling incredibly confused. "Does he hurt you in these dreams?"

Ignatius stopped his pacing and gave Kate his most ugly glare, "I do not dream!" He was getting really tired of the whole thing. "I am not this John Sheppard. I will not repeat it again, I am not John Sheppard!" To give his statement a little extra power, Ignatius kicked his cot hard enough to break it.

Kate jumped at the sudden display of violence and tried effortlessly to calm the man down again. "Ignatius, please calm down."

Ignatius felt like taking all his frustrations and anger out on the cot. He really needed to clear his mind and figure out what was really going on with him. He knew the doctor was right, but he wasn't going to be able to clear his confusion of his real identity with them in the neighborhood. He had to go back to the place he loved during the day and despised while he was asleep. He needed to return to the Genii.

Ignatius kicked the small cot with all his might, a plan already forming in his confused mind. Maybe the doctor wanted to talk to John Sheppard... maybe she would.

Kate knew that no matter how aggressive Ignatius would become, they couldn't afford opening the cell, "Please Ignatius, we don't want to hurt you."

The small cot was now broken, Ignatius grabbed one of its metal legs and started smacking the shield with it. By now Kate had forgotten all about her plan, "John, stop it!"

And to everyone's surprise, he did stop. Ignatius fell to his knees, the metal leg in his hands. He was looking at it with a peculiar interest. Kate noticed the sharp edge of the item in John's hand.

Then he suddenly spoke up, "I can't do this anymore, Doctor. I don't want to close my eyes and relive all the tortures Kolya put me through."

Kate blinked and did a double take, "John? John, you have to fight it. Please, let me help."

"You cannot help me." John didn't take his eyes off the sharp metal in his hands. Then without any warning, he placed it in his neck, right by his jugular, "I don't want to live like this anymore."

Kate's mind was racing. She couldn't let John take his own life for the only reason that she was too scared to open the cell. She desperately looked at Sgt. Stackhouse, "Open the cell, don't use the stunners unless it is absolutely necessary."

Stackhouse hesitated, "Doctor?"

"Open it up, now!" Deep down Kate knew it was wrong, it could be a trap but she had to take that chance.

The moment the door opened, Kate walked in slowly towards the kneeling figure of John. He still had the sharp metal against his neck. Stackhouse approached slowly from the side, his stunner at the ready.

Kate tried to make eye contact, "John, please look at me, you don't have to do this." She noticed the metal was already cutting John skin and had to swallow. She really needed to make some contact with him if she wanted him to surrender the metal rod. But before she could even say another word, John swung the metal in his hands and slammed it against the back of Stackhouse's knees. The young airman buckled over and landed hard against the floor, his head hitting the chair Kate had been using, knocking him unconscious.

He acted so fast that nobody was prepared for what came next. John grabbed Kate's wrist, snatched her pen out of her hand and pulled her close to him, stabbing her twice in the ribs right under her arm. Kate screamed in pain as the now obvious Ignatius grabbed her by her neck and pointed the bloody pen to her main vein.

Ignatius looked frantically around the room; there were two more soldiers to deal with. They were pointing their stunners at him, trying to find the best shot.

Ignatius in turn pressed the bloody pen tighter against Kate's vein and shouted, "Careful! If you try to stun me I'll have enough strength to do one last strike. You'll only condemn this nice doctor to death. I swear either of you try anything and this goes straight into her neck!"

All color had drained from Kate's face and she was paralyzed with fear, hoping the men were not going to shoot. The two airmen looked at each other, their movements slow and calculated. One of them tried to turn his radio on, while the other moved slightly to the side to try to get a clear shot at Ignatius.

But they had underestimated him and before they could react, Ignatius dropped the pen and grabbed Stackhouse's 9mm. In one movement he shot them both without a second thought.

Ignatius still had a firm grip on the doctor; feeling his victim shaking slightly and seeing a red stain appear on her shirt. Ignatius used her as a shield and moved with her towards the exit. Once outside he headed towards the transporter, pressing the destination he wanted to go. He smacked the doctor on the back of her head with his gun and walked out when the doors opened, leaving a very unconscious Heightmeyer in the small space.

From the transporter he cautiously made his way into the Gate room. He managed to stay out of sight and when he finally walked into the control area, there were only a few people around. There were two technicians typing away on the consoles and two soldiers by the gate. Ignatius made his move and walked towards the technicians. He took them completely by surprise and in a just two seconds flat they were lying on the floor out cold.

Ignatius looked through the screens. He knew if he activated the gate that there was little to no chance of actually getting through. A plan started forming in his mind as he looked through the city's life sensors. He saw what he needed to see and by that time the two soldiers downstairs had noticed Ignatius. They were quickly making their way towards him, one of them activating his radio on the way.

Before running off, Ignatius did the one thing he could think off, shutting down the console that regulated the life sensors, making him invisible to them and making it harder for them to find him.


	11. Last Resort

**Last Resort  
**

Elizabeth had retreated to her room in an attempt to try and do her work in a more private place. Where she had no one bothering her with trivial things or wanting to talk to her about what was going on with the Major. And she certainly didn't want to hear one more person saying that she needed rest or let others take of matters. She acknowledged she was tired but she had gone like this before. It didn't matter to her as long as she could manage keeping her mind occupied in something not related to the current situation.

Unfortunately for her the universe decided differently when a call from the Gate room informed her that John had escaped his cell and had attempted a futile escape through the Stargate. The Sergeant on duty also told her the man had rendered one of the consoles useless, knocked two technicians unconscious but had run away as soon as the guards had spotted him. John was now on the run and possibly dangerous too.

She dropped her papers and quickly got up, making her way over to her door which opened in front of her only to reveal the run-away.

She gasped and immediately backed away further inside her room, almost tumbling over some of her carelessly dropped shoes. The thought of calling for help did cross her mind but she knew he would stop her. She jumped again as she heard Rodney's voice coming heavily through the radio, a dread sense of déjà-vu overtook her senses.

Ignatius walked into the room, almost sensing her fear for him. He didn't even have to say one word to intimidate her. Then again he knew he must be looking like he was about to kill her, and that was not that far from the truth either. He continued to close the distance between himself and the woman he wanted to despise so much.

Elizabeth didn't need to look back to know she had reached the far end of her room and that she had nowhere to go anymore. Nothing prepared her for what came next as John grabbed Elizabeth by the front of her jacket with one hand while he hit her square in the face with the other. Ignatius caught her before she hit the floor, lifted her over his shoulder and carried her out of her room and away from that part of the city.

-0-0-0-0-0-0-

Rodney had spent most of his evening in his lab. He hadn't been really working, just checking on his fellow scientists, bantering a little with Zelenka. All he was doing basically, like most people in Atlantis, was keeping his troubled mind occupied. Zelenka had caught up on his mood and had gently kicked him out of the lab, telling him he should get some rest. He had agreed without much complaint, knowing if Carson would find him there in the middle of the night he would send him straight back to the infirmary and would keep him there until his wound had fully healed. That was something Rodney didn't really look forward to, in fact he hated sleeping in the infirmary.

It had been two days since he had talked with John, and since that conversation he hadn't heard of any improvement whatsoever.

Rodney decided that before going back to his room he could afford to pay John another visit. He had just approached the transporter when the city's alarm went off and he got the news John had escaped and was now roaming Atlantis. He blinked and at once his heart skipped a beat as he remembered Kate had told him she was going to try and get through to the Major.

He gulped the dreading feeling down and quickly opened the doors of the transporter, coming eye to eye with an unexpected sight. There she was, his Kate, lying uncomfortable against the side of the transporter, unconscious and a dark red stain covering the right side of her white shirt, making it look even more horrifying. Rodney quickly kneeled besides her, wanting so much to touch her, feeling if she were still with him.

"Oh no! Kate!" He felt panic rise in his chest, swallowing hard as he noticed the blood had already dripped onto the floor of the transporter, forming a small puddle underneath her. He softly touched her face, fearing it would be cold to the touch, but instead he felt movement as Kate turned into his touch. Semi-conscious she struggled to talk to him, assure him she was okay while the guards downstairs weren't.

"Rodney..." her speech was slurred and he could hear her struggle against unconsciousness, "John... guards... shot..." Kate's head lolled backwards as she was loosing the battle rather quickly now.

"What?" Rodney forced her to look up at him but her eyes were glazed over and he knew he had to keep her awake some how, just long enough for him to find out what she meant. "Kate! Come on, stay with me." He shook her shoulders a little, forgetting for a second he could cause more damage that way.

"Can't..."

He knew he couldn't wait any longer; in fact he should have probably done so the moment he found her, but his mind was too occupied. He fumbled for his radio and practically shouted for Beckett to get his medical ass to the transporter he was at ASAP.

"Rodney..." Carson came flying around the corner, skidding to a halt in front of the transporter. A small team of medics and nurses had been following him and stopped right behind him, waiting for his orders.

"The brig..." Rodney remembered Kate had tried to tell him something before she had gone into shock.

"I have a team on the way," Carson replied quickly.

Rodney shifted away, reluctantly leaving the psychiatrist in the more than capable hands of Carson Beckett.

They managed to get her stabilized enough to roll her to the infirmary where they could treat her better. Rodney stayed close by and followed the team as soon as they moved. Although nearing the infirmary Carson asked Rodney to stay outside so he could do his job properly, without having to worry about a concerned friend. But McKay wouldn't listen and hurried inside with the rest of them, positioning himself in a way he could follow every movement up close.

"Carson, I think there are injured soldiers down at the brig."

"One of the other doctors has that area covered, Rodney." Carson turned his attention back to Kate while Rodney backed away a little, letting the doctor and his team do their job.

"Is she going to be okay?" Rodney still hovered rather close by.

Without looking up from his work, Carson replied, "She has been stabbed with something small but sharp. She has lost a lot of blood and I am sure her she's suffering from a collapsed lung," he finally looked up at Rodney, giving him a reassuring look. "She will be fine, Rodney, thanks to you. You found her just in time," Carson looked up again and he noticed McKay turned rather pale and seemed to be drained of all his energy. "Rodney, are you ok?"

Rodney was startled by Carson's words. The doctor shouldn't be worried about him this moment. He nodded, "I'm fine."

With those words he turned around and all but ran out of the infirmary. Rodney's mind was racing, the image of Kate's blood-stained body dancing around in his head. Another feeling of dread pushed itself in first place when he realized something much worse. "Elizabeth…. Elizabeth, please answer me!" His heart was racing alongside his mind. What if something had happened to Elizabeth? He had to find her.

He quickly made his way to the control tower where he met with Sergeant Bates, who he immediately called to attention, "Sergeant! Have you seen Dr. Weir?"

"No, she answered our call when Major Sheppard appeared in here. She said she'd be here in..." Bates cursed softly and quickly turned his radio on and tried to reach the Commander of Atlantis again. They received nothing but static and at once they knew they had a huge problem. "Damn it!"

"He has her." Both men came to the exact same conclusion at the exact same time, looking at each other for a plan.

"Damn it! Lt. Ford, come in!" There was a moment of static before Ford's voice was heard over the radio.

"Sir, we have a problem." Bates looked from Rodney to the Stargate in front of him, patiently waiting for Ford to reply.

"Tell me about it! Hatfield, Stackhouse, and Cortez were shot. And I have no idea how he managed." Ford was in utter disbelief, as he had thought it was rather impossible for someone to escape from the brig.

Rodney interrupted the conversation, "He used Dr. Heighmeyer, probably as a shield and used her to escape. She's in the infirmary."

They could hear Ford sighing on the other side, "Sgt. Bates, gather a team and start searching the living quarters and the labs." But before Ford could finish, Bates interrupted him.

"Sir, we think... no, we are, actually, convinced Major took Dr. Weir."

Ford cursed loudly, "Sergeant, gather as much men as you can find and start sweeping the city. And send a small team to Dr. Weir's room just to be sure he has her."

"Yes Sir." Bates looked at Rodney and signaled up the stairs, "With me Doctor."

Once they arrived up the stairs and into the control area, Rodney could see the chaos John had created when had disabled a few consoles. "What happened here?"

"Major Sheppard disabled the city's life sensors. If we go out and look for them, we only have the small ones, not the city wide sensor."

Rodney moved in front the dead console and panel. He touched the keys but nothing happened, confirming the Bates' statement. McKay cursed softly as he knew that by now John knew exactly what he was doing and for some reason it involved Elizabeth.

Memories from the moment Kolya had threatened them during the storm, and his particular interest in Elizabeth, came floating back to the front of his mind. He shook his head in an attempt to shake them back to his subconscious mind. He suddenly felt like the world was too much to carry and he had to steady himself.

"Dr. McKay, you ok?" Bates looked at Rodney and noticed how all the color had drained from the man's face.

Rodney pulled himself together, taking a deep breath in an attempt to settle his mind at ease and in order to have Bates think he was okay. "I'm fine. Just gather your team and get Grodin and Zelenka here, to work with me."


	12. With You

**With You**

Ignatius had no idea what had driven him to take Elizabeth Weir with him. Maybe it had been because he kept hearing Commander Kolya's voice in his head, reminding him to bring Elizabeth to the Genii. It was like every time he began doubting who he was, the order of bringing Elizabeth to the Genii surfaced.

He shook his head in an attempt to clear his mind and looked around. He had brought her to an empty room in an unexplored part of the city. She was still out cold, and by now Ignatius was sure every single person in Atlantis was looking for them. He knew that they couldn't stay in that room for long.

Ignatius' worries momentarily faded as he felt tiredness sweep over his body. He sat down on the floor, facing Elizabeth, and closed his eyes. Without even realizing it, he fell asleep, where a dream was formed almost instantaneously.

Ignatius was outside in a field, the grass feeling soft under his bare feet. There was a soft breeze, almost comforting. So he walked up a hill and looked out of over the rest of the field. He could see a Stargate in the distance.

Suddenly shouts came out of nowhere as four people were seen running towards that same Stargate, a woman and three men. Ignatius ran towards them, his curiosity getting the better of him as he really wanted to see who they were. Once close enough, he realized that it was Teyla, Lt. Ford, Dr. McKay and…. himself, dressed in the standard Atlantis military clothes.

It was an awkward moment for Ignatius to see himself as the very person he had been denying to be. He kept a close watch on the group and saw the first two opening up the gate and going through. Ignatius ran closer; he wanted to be able to hear what they had to say that could help him with the mess in his head.

He now saw Lt. Ford running towards the gate but he suddenly stopped and looked back, his weapon at the ready. Ignatius saw himself running and shouting, "Go! I'll cover you." Ford stepped through the gate, and Ignatius saw himself getting really close to the DHD when a dart hit him in the back of his neck. He slowed down and seemed out of breath. Ignatius moved closer to himself.

Ignatius was now so close by, that he could reach out and touch the other man.

But Ignatius felt like he was watching a loosing battle when he saw himself struggling to get to the gate. It was so close, but so hard to reach. He looked around just in time to see a bunch of people running towards the gate. Ignatius returned his gaze towards himself. The other him was almost at the gate, crawling towards it while his hand could almost touch the blue shimmering pool, when someone came from his side and kicked him away from the gate.

The gate shut down, and Ignatius saw Commander Kolya stopping at the side of his other self. Ignatius was almost convinced that it was really himself. Kolya crouched down and smiled, "Major Sheppard! So good of you to join us."

Sheppard gave Kolya a murderous glare, "Kolya, we had a deal."

Kolya smiled, "The deal's off."

Ignatius noticed himself struggling to stay awake, "You'll soon be dead."

"I don't think so." Then Kolya took a small gun out of his vest and shot another dart into Sheppard.

Ignatius saw how his other self gave into the need for sleep and was quickly taken away by Genii soldiers. He felt so helpless, wanting to do something so badly, but he was just a mere spectator in a place that should have never existed.

-0-0-0-0-0-

The moment Elizabeth started to regain some form of consciousness she felt like all of it had just been a bad dream. Her mind expressing her fear in a nightmare, a very real nightmare which had her believing John had walked into her room, knocked her unconscious in order to drag her along as his hostage. It wasn't until the pain hit her face moments later that she began to understand it was too real to be just a dream. She started probing her face, in order to locate the source of the stinging pain. She hissed as came in contact with a particular soar spot and retracted her hand, noticing something sticky attached to her fingers. After a closer look, she identified the substance as blood, her blood. She touched her face again, gently probing around the soar spot, and found that the blood was coming from her nose.

Elizabeth stopped probing; deciding for the best not to do any more damage than there already was and looked around trying to figure out where the hell he had taken her. She almost gave a little yell when she noticed him on the other side of the room across from her, slumped against the wall seemingly asleep. Though his eyes were firmly closed Elizabeth couldn't be sure if he was really asleep.

Slowly so as not to disturb him, she got up. A twirl of dust rose as she did and therefore she figured they were deep within the city, probably in some unexplored area of Atlantis. She walked towards the door and tried to open it but as she half expected it, it was locked.

"You didn't think that I would leave it open, now did you?"

Elizabeth was momentarily startled by John. She quickly turned around to face him and noticed he was already standing. "Why are you doing this?"

"I need to make things right, I need to clear this up."

"You don't have to! Do you really think Kolya is who you think he is?" She knew she had to somehow convince him or else she was going to in a lot more trouble than she was already in.

"I don't know anything anymore. That's why I need to go back, I have to be sure."

"Sure of what? Of who you are? We can help you, can't you see that? You don't have to go back there."

Ignatius started to walk towards Elizabeth, "Oh, yes, I have to."

Elizabeth gulped visibly and desperation was setting in. She really didn't want to know what would happen if Ignatius took her to the Genii. "Why? If you don't know anymore… if you are in doubt, why go back there?"

"Because I have to get rid of you! So I can control the doubts. Every time I doubt myself, I'm kept being reminded that I should take you to him."

Elizabeth stared at Ignatius wide-eyed, recalling the moment Kolya had tried to take her to the Genii. Maybe that was what it was all about. The look on Ignatius face suddenly changed and it scared her senseless as his last words directed at her came to her mind, _"I wish I could be there, when he's breaking you."_

That sent a shiver down her spine and she started back away from him as far as she could possibly get. "Ignatius, there's no need for that."

Ignatius looked at Elizabeth in mild amusement. He suddenly remembered their last conversation and noticed the fear that was building in her eyes. He started to move closer, "I want everything to stop; I want to return to normal. Whatever normal is, and the only way to do that is to take you to him."

Elizabeth flinched and Ignatius saw it. He smirked and closed the distance between them even further, "Are you afraid of what he might do to you? I wasn't lying the other day, he will have you."

Elizabeth kept walking back until she felt one of the walls against her back. But Ignatius didn't stop and kept coming closer, invading more than her personal space. She tried hard to keep her look straight at him, "Don't do this!" She was pleading with him now. "How can you talk like that when you once tried to kill Kolya?"

"That won't work this time." He continued walking closer, "Why Elizabeth… are you afraid?"

She tried unsuccessfully to gather all her courage, "No..."

"I don't believe you. I can see it in your eyes." The space between them was getting smaller, until he was pressing her against the wall behind her. Somehow his leg went in between hers, placing a hand on her cheek, "Would you rather have me do it?"

Elizabeth felt herself tremble. He was so close it was frightening her to death. His words were imprinted on her, "Don't do this John, you know this is not you."

Ignatius smirked; he was only doing it for the sake of a good scare. He mused as he opened up her jacket, slowly revealing her red shirt underneath, "There is nothing left for me, I am giving you a choice. Either way you'll have to go through with it."

Elizabeth's mind was racing; she didn't want this to happen. _'Who is this monster I'm talking to?"_ Elizabeth decided to press on, knowing all too well she had to stall him. "You don't have to do this John! Why follow the orders of a man you once tried to kill?"

His features changed as fast as they had earlier, "That never happened!"

That had snapped something in his mind as all of a sudden Ignatius went all savage as he started to rip her jacket off. She tried with all her will to stop him, but he slapped her square in the face and threw the jacket to the other side of the room. Elizabeth tasted blood in her mouth and desperately tried to get some space between them, but he was so much stronger than her, "Come on John! You saved me from Kolya, that's why you shot him. There is no reason to do this!"

Ignatius' face filled with more anger and it seemed the more she said the angrier he got, "Another lie! Why can't you say that all you really want is to turn me!"

"No, that's not true! Search within your mind! You'll see it. I was in the gate room and Kolya was pulling me towards the gate and you..." He had enough and grabbed her throat with all his strength, effectively shutting her up. Elizabeth started struggling against him, kicking him, but as a result both of them slid down to the floor, where Ignatius remained on top of her. He pinned her down, choking the life out of her.

Ignatius tried with all his might. It was as if by killing her, everything would stop. Elizabeth started to move slower, her fight weaker. Her lips turned a lighter shade of blue while her eyes never left his. Suddenly Ignatius found himself staring at her while a sudden flood of memories crept out and swept everything away.

Like a tsunami they reached for the darkest corners of his mind, and at that moment Ignatius and John were one. Not really sure who was who; he looked down at Elizabeth and saw that he was killing her. She was barely conscious when his hands left her throat in one quick move; the same that made him stumble away from her. She gasped for a moment, only to go completely limp the next.


	13. Thoughtless

**Thoughtless**

They had been working on the console for more that an hour without a single result, bringing their frustrations to unknown heights. Zelenka was taking readings on a computer while Peter was working with the panels and the topside of the console. Rodney had somehow managed to get under it to work with the interface cables and the consoles inside but so far not even someone with the ancient gene could turn it on. Everyone was so engrossed into their work that when Rodney suddenly cursed out loud, they all jumped up startled. "Damn it, Sheppard!"

A minute later, Rodney squeezed out from underneath the console and pulled himself up from the floor. Once he was up he quickly had to reach out for a chair so he could sit down and prohibit the dizziness from taking over completely. His injury was stinging and the pain was creeping up again. This time, however, he didn't know if he could deal with it on top of everything else. He heard his name being called from really far away and turned in the direction of the voice only half registering what was said. Dr. Zelenka and Sgt. Bates were looking at him, worry visible in their eyes. "Dr. McKay, are you feeling ok?"

Rodney looked up and took a deep breath, wincing slightly as his body objected. "Did any of the teams find anything?"

"No, but we're still looking. There are three teams out and three that are about to go into unexplored sections. Don't worry, we will find them." Bates, who still had his arm in a sling, took the sling off and stretched his arm slowly, testing its use. He winced and his face momentarily filled with pain. He looked back at Rodney, who he noticed was looking worse by the minute.

Zelenka immediately stopped working and almost ordered Rodney to go to the infirmary, "Come on Rodney, you're no use to us if you drop dead. Go to Dr. Beckett, maybe you can come back and help us later."

"Do I have to remind you that crazy psychopath "Ignatius" is loose in the city with Elizabeth Weir as his hostage? Who knows what he'll do to her!"

Bates cut the conversation short, "Dr. McKay, there's people searching already. Lt. Ford is gathering a new group as we speak. Go to the infirmary, we'll keep you informed!"

Right then another stabbing pain went through McKay's chest and send him bending until his face almost touched his knees. There he noticed a small stain forming on his jacket, which he immediately recognized as blood, his blood. His mind went into overload and as a result he decided for the best to leave for the infirmary. As discreetly as he could he sat up straight and got up, crossed his arms over his chest to block the small stain and excused himself. "Ok, but please stay in radio contact."

He reached the infirmary without fainting for which he thanked every god in the universe. As he walked in he spotted Carson looking over someone's chart. Rodney looked around the infirmary, which was now almost at its full capacity. Carson spotted Rodney by the door and immediately walked towards him. Rodney was still covering his chest when Carson arrived at his side, "How's Kate doing?"

Carson's face turned grim, "Not so good, she went into shock shortly after we brought her here. She had a punctured lung, which we were able to fix. She's resting now."

"What about the others?"

"Stackhouse had a concussion and a sprained knee. Airman Cortez has a bullet wound to the chest near his collarbone. He was very lucky; the bullet missed a lot of dangerous areas. And Sgt. Hatfield is in critical condition with a wound to the stomach," Carson looked Rodney over, "What about you?"

"Well..." Rodney hesitated for a second, "I have to show you something," he moved further into the infirmary, with Carson close behind. Once he was far enough and sure nobody else could hear them, Rodney put his arms down and opened his jacket. When Carson saw the bloodstain on the scientist's shirt he scoffed, "Oh, damn it Rodney! Why can't you come straight to me? When did this happen?"

"I don't know, I just noticed it." Rodney didn't dare to look up at Carson, knowing he was right, and kept his gaze fixed on the wall behind the Doctor.

Carson was visible angry, "Take that damned jacket off!" Once Rodney took the jacket off, Carson snapped, the whole front of the shirt was covered in blood and he had a smaller stain on the back. "That's it; I'm keeping you here until the end of the month!"

Rodney's eyes went wide. "No!" he uttered desperately, "I'm needed back at the command center, so just change the bandage and I'll be on my way!"

Carson was about to snap again at Rodney when a call came from the gate room.

-0-0-0-0-

Elizabeth was lying on the floor, deadly still. He still couldn't believe what he had just done. His mind was on overload and all he could do was move away to the opposite wall. He pressed his knees to his chest. In his mind she had died when she had gasped for that last bit of air. She was dead and he had killed her. He covered his face with his hands as involuntarily tears starting running.

This was no longer a matter about which he was, John or Ignatius. It didn't matter anymore. He had killed her. His mind was racing. He looked around and found the gun he had taken earlier from Stackhouse. That reminded him of the mess he made down at the brig. He had hurt all those people ... Cortez, Hatfield, Stackhouse, and Kate Heighmeyer.

It was at that moment that he understood it had always been him. Ignatius, John, they were the same person. He couldn't explain it but he knew it was the only way. No matter who he was he had always the feeling of someone wanting to brainwash him. With that feeling in mind he grabbed the gun and stared at it. Maybe it was better to end it all than to deal with the mess in his head. After all, he wasn't strong enough. That had now been proven to him.

He placed the gun against his forehead and closed his eyes, tightly. And there he stayed, feeling the cold metal against his head. He couldn't stand the overwhelming feeling he had within him. But then it started to make sense, all of it as if he had finally found the switch to the proverbial light bulb. He watched as he saw himself being ambushed near the Stargate, being beaten and interrogated. After that everything changed, they started doing different things; they tried to make him feel inferior, the recordings, the electrical shocks, and the ice baths. Until that day, where all they did was putting a device on his head and everything went to hell. That day everything changed.

He put the gun down and stroked his beard, thinking. Kolya... that bastard was going to pay, one way or another. He knew that killing Kolya wouldn't erase all the atrocities he had just committed. But it would give satisfaction to his heart the knowledge and the memory of seeing Kolya dying by his hand. And finally figuring out for certain the feeling that he was, and would always be in fact John Sheppard.

It was Kolya's fault that he had caused all the damage he'd done. To a bunch of people that didn't even deserve such pain and fear. He looked at Elizabeth once more. Her limp body was what screamed to him to settle things right, at least for just this once.

His mind slowly came up with a suitable plan of how he was going to do this mission. He wasn't sure about the whole idea just yet but since he was constantly reminded of going back to the Genii home world he thought it might just be the place to start from. With that thought in mind he got up, walked towards Elizabeth and gently picked her up, carrying her in his arms he walked out.

Up, down, then through a transport, until he reached the entrance of the jumper bay. Right at the door, two soldiers were standing guard blocking his way in. He decided to turn around without making noise and alert to the two and find the other entrance few people knew about. He made his way through a dark hallway, where he had to evade one of the teams. They had a life signs detector, which meant they would find him soon if he didn't keep moving. Then he found the door he was looking for and walked into the deserted Jumper bay. He quickly made his way to the closest jumper available and walked inside, placing Elizabeth on the bench in the back of the jumper. He took a seat in front and quickly turned the jumper on, remembering all too well how to fly one of them. He looked to the center of the bay and opened the hatch in the floor through which he could reach the gate room.

-0-0-0-0-0-0-0-0-

Radek Zelenka and Peter Grodin were still working on the console when suddenly one of the panels came to life. Both men looked up and stared at the screen. Grodin pressed some keys of the console to get the life sensors online, but instead they heard a shout coming from the gate room.

Zelenka got up and looked down where Sgt. Bates was looking up, "Raise the shield!"

The gate activated and before Grodin or Zelenka could reach the shield activation button the jumper was in the room and halfway through the gate. All happened in just a couple of seconds and before anyone could react properly the jumper disappeared through the open wormhole.

Bates ran up the stairs and shouted, "Where did he go?"

Zelenka looked to another computer screen nearby and saw the address before the gate shut down. When silence returned, Zelenka glanced at Bates, not really believing what he had as answer, "The Genii home world."


	14. Going Under

**Going Under**

The puddle-jumper flew through the other side of the wormhole into a sunny day on the Genii home world, but he did not noticed. His mind was set on just one thing, something that had to be done now or it would haunt him forever.

Finding Kolya's house wasn't all that difficult. It felt so familiar to him that it felt as if he had always known where it was. He slowly landed the cloaked jumper near the house, which looked nothing different from any other Genii house.

He took the remote but didn't turn off the cloak when he walked out, Elizabeth securely in his arms and a gun stuck in his trousers, the cold metal poking in his bare back. He didn't knock; he just burst straight through the door, hoping for a surprising effect.

-0-0-0-0-0-

If Atlantis had been buzzing with activity before, it now felt like a constant humming. Military teams were getting ready, with people walking back and forth. Ford was in charge now, and he had called an emergency meeting in the briefing room. Sgt. Bates, Teyla, Dr. McKay and as many soldiers they could get inside the room, were present to listen and help wherever possible.

Ford glanced around, "So what are our options? Are we sure Dr. Weir is with him?"

McKay sighed and replied, "As of yet that isn't confirmed, meaning that the sensors haven't picked up her life sign. So either she's ... dead or with him. Both those options are bad, but death is worse in my opinion."

At that Teyla put in her two cents, "We should go to the Genii and get them back."

Bates eyed Teyla while he replied, "But before we even consider that, we need to make sure no one is waiting for us at the gate. And at this point, any sort of rescue plan is to get Dr. Weir back, preferably alive and in one piece. We should make clear that as of now Major Sheppard is no longer our first priority and should be treated as such."

Soft muttering rose in the crowd, everyone having his or her own opinion on Bates' though concerning the Major. Ford was the first to speak out loud, "Major Sheppard is as important as Dr. Weir."

But McKay cut him short, "Bates is right, we have to assume that by his actions Sheppard is putting the Genii before anything else. If we can get them both back that would be nice, but we don't know what happened at the brig and therefore no idea what made him snap like he did. We can only assume he has chosen a side, and it isn't ours."

Every single person in the room remained quiet, not knowing how to answer or what to say to McKay's statement, since they all knew he was probably right.

-0-0-0-0-0-0-

Acastus Kolya was having a drink with one of his comrades, when the door was kicked open with a loud bang. The Genii Commander was momentarily startled when he saw the man that walked in. He looked at his partner, who had a gun at the ready but ordered him to stand down.

Kolya smiled, stood up and carefully spoke up, "Ignatius, I thought you were dead."

Ignatius remained standing at the door while he replied in an ice-cold tone, "Now you see I am not. She, however, is ... dead." He finally walked into the room and gently placed Elizabeth on a nearby sofa.

Kolya frowned, and he carefully moved around, glancing suspiciously at Ignatius. Then he turned his attention to Elizabeth and walked towards her. Kolya eyed Ignatius again; he clearly had questions, but decided to play it cool for now. Kolya touched Elizabeth's face and looked her over.

John was giving Kolya a stare which, if stares could kill, would have send him off to the eternal hunting grounds by now. His face was cleared of all emotion, not giving anything away. Not yet anyway since he wanted to hear the words out of Kolya's mouth. And Kolya talked, but it was a revelation John hadn't expected to hear.

"She is not dead."

-0-0-0-0-0-0

The MALP was already set up in the gate room. Peter Grodin dialed the address while the rest of the people gathered around the control area, waiting for some results. The Stargate opened with the usual swoosh and the MALP was sent on its way. An image appeared on the screens not much later, showing approximately 10 people gathered around the gate. One of them shot the MALP, effectively deactivating it.

The gate shut down, while they all glanced at one another, sighing as they knew they had to come up with a really good plan if they were ever going to want to get Dr. Weir and preferably also the Major back alive and in one piece as Bates had requested.

-0-0-0-0-0-0-0-

"You were supposed to kill the team that night!" Kolya fumed, "Those were your orders but instead you disappear and come back with a half-dead woman. Yet I specifically asked that Dr. Weir should be brought to me _alive_!" Kolya looked like he was ready to kill John.

John didn't show a single emotion as he replied, "I was captured and she wasn't on the planet that night. I guess you should have checked your Intel before sending someone on a mission like that."

Kolya eyed him suspiciously, "How did you manage to get here?"

"Every single person who stood in my way has suffered the consequences." John returned the stare the Genii was giving him, equally as deadly.

Kolya moved in closer to John, "I imagine you came here by ship. Where is it?"

John shifted, risking a quick glance outside, "Hidden."

"Why?"

"For protection."

Kolya stayed silent for a moment, and then he looked at the other man in the house, "Leave us!"

The man put his gun away and walked out of the house, closing the door behind him. Once alone Kolya walked towards his table and poured himself another drink. "I am surprised that they actually weren't able to keep you there."

John relaxed a little and approached the table tentatively, "They tried, believe me, they tried. They tried other things as well."

Kolya took a swig of his drink and sat back down in his chair, "They did?"

"Yes... they tried to make me believe I was a man called John Sheppard."

At that statement, Kolya looked up, "And did you believe them?"

"No! I didn't believe anything they said. And they really tried to make me believe it."

Kolya looked down, stood up and walked to one of the cabinets, "Sorry to hear that." He turned his back to John, fumbling with the doors of the cabinet.

John moved in a little closer towards Kolya, "But the thing is that the moment I started remembering, everything changed."

Kolya froze, "Did it?"

"Yes, because the moment I remembered you ambushing me by the Stargate, it clarified the one thing I needed to know and was looking for the whole time they had me jailed."

Kolya now appeared to be speaking through clenched teeth as he said, "And what was that?" He turned around at once, only to find John pointing a gun at him and to his own fear firing it.

John didn't show any sort of emotion, "I _AM_ John Sheppard."

-0-0-0-0-0

Breathe … in … out, her body was making that her primary conscious command. Her brain was all fuzzy, though she was aware of people talking. She recognized the voices and a wave of momentary fear rushed through her mind, Kolya and John. She felt someone touch her face and Elizabeth couldn't help but shiver a little.

She struggled hard to stay conscious but couldn't really prevent from drifting in and out of semi-consciousness. Her breathing was ragged and very slow, but she did manage to open her eyes, if only a little bit. The sight that met her was tense and frightening, Kolya and Ignatius were talking. Then the Genii soldier turned and walked towards a cabinet. Their conversation was unclear, but Elizabeth saw Kolya taking out a gun.

But when Kolya turned around she got a better look at what Ignatius was holding, a gun pointed straight at Kolya. He raised the gun and the shot rang in her ears. All through the ringing she could hear him yell something at Kolya, who was looking at Ignatius wide-eyed, surprise written all over his face. _'I am John Sheppard.'_

Elizabeth willed her mind to register the words and their meaning. That it was indeed John Sheppard who was yelling them and not some figment of her imagination or an unexpected hallucination from being oxygen deprived.

Kolya stumbled backwards; he hit the cabinet and sank to the floor. All the while looking up at Sheppard and feeling his warm blood seep through his fingers of the hand covering the bullet wound.

The man that had been kicked out earlier suddenly stood in the doorway, clearly alarmed at the gun firing. Not that he knew who had shot who, as he knew Kolya didn't like betrayal, and certainly not from Ignatius.

Sheppard turned around at once, as he caught sight of the man and immediately put a bullet in between the man's eyes, effectively killing him. That thread gone he turned back to Kolya.

-0-0-0-0-0-0-

John noticed Kolya was still holding onto his last bit of strength, trying fiercely to keep himself from dying. Sheppard kneeled down beside him and without a moment's thought he put the gun to Kolya's temple. "Tell me what you did to me and I will end it quickly!"

Kolya's breath was ragged, "There is no point … you are already free ... free from it. I guess I under...estimated you after a-all."

But that wasn't the answer John was looking for and he forcefully grabbed Kolya's shirt, pulling him closer while screaming with all his might, "What the fuck did you do to me?"

Kolya stared up at John, more and more blood dripping onto the floor underneath him, "The usual techniques for mind ... control weren't working. So we used a m-machine that rearranges the subject's personality. But none of it matters n-now, you didn't do what I told you ... to do and I don't think my people will allow you to leave with her ... especially after what you have done... to me."

John risked a glance behind him and was surprised to find that Elizabeth eyes were opened and who was willing herself to keep looking at him. He then knew his life wasn't the only one at stake anymore. A loud sound filled the room and he felt something fast and hot on his chest. John didn't flinch; instead he hit Kolya square in the face and took the gun away from his hands. Kolya fought for it, but at that point John was beyond rage and he fired his gun, sending a bullet straight through Kolya's heart. His cold eyes glazed over and his body went completely limp while the blood spattered all over John.

For just one tiny moment there was complete silence, before all hell seemed to break loose at once. John quickly made his way over to Elizabeth, picked her up and walked out the door. Once the door was opened Sheppard noticed he could easily make it to the jumper, killing a few people on the way.

He ran for it dodging bullets as he went, hoping none would hit target, uncloaked the jumper and sprinted inside. As soon as the hatch closed he placed Elizabeth against it, knowing she would at least be somewhat comfortable. He ran to the front, turning the jumper on. Through the window, he could see the Genii soldiers running towards the ship, but they were fashionably late as the jumper took off and John flew it straight towards the Stargate.


	15. Breaking the Habit

**Breaking the Habit**

Sergeant Bates, Teyla and a full military team were gathered in the gate room. Their plan was to use a jumper as a decoy to clear the path. A full military team would follow the ship onto the Genii home world and would try to get their people back. They knew it was a rather dangerous plan, which could still lead to enough casualties but they had to try something.

Lt. Ford and another team were inside the Jumper. They had decided to take as many people as possible but without leaving Atlantis completely defenseless. For now, everyone was just waiting for the go ahead from Ford. Having that responsibility now, Lt. Ford did the job without question.

He walked in the jumper and informed the pilot to be ready. Then he walked back out and went straight to Rodney, who was at the bay doors, "Dr. McKay! I don't know how this will go. But have the gate room cleared at all times. Hopefully we'll be back by dinner." His attempt at a joke was lost on McKay and the others, and Ford only curtly smiled.

The only thing Rodney did was nod, acknowledging Ford's order. In turn Ford activated his radio and started giving last minute details about the plan to Sgt. Bates, who made sure the others, would know as well. They were talking to one another when the gate suddenly activated with an incoming wormhole.

Bates clicked his radio and sprinted upstairs towards the control center, ordering everybody to clear the gate area and take defense positions. "Lt. Ford, we have gate activity! Raise the shield! Do we have an IDC?"

Peter looked anxiously at the screen of his computer, "No, but we have a transmission coming in."

"Patch it through!" They were met with silence until Sheppard's voice came through.

"Atlantis, this is Sheppard, please lower the shield."

Bates looked doubtful and thumbed his radio. "How do we know it's really you and not some contingency of Genii soldiers?"

"Bates, lower the damn shield!"

"Sir, I can't do it. Where is Doctor Weir?" At that moment Ford joined Bates in the control area, as he had left his jumper as fast as humanly possible.

"Please, I'm coming in hot and Elizabeth needs medical attention. You can storm the jumper once I'm there, for all I care, but please let us in. I don't care if you throw me into the brig for the rest of my life. But I am one minute away from the gate and I'm going in with or without your blessing," Sheppard made himself very clear and Bates knew that if he was indeed going to enter the wormhole without having the shield out of his way, they would loose all hope of ever seeing Weir alive again. Ever see her again would already be a problem then.

Ford nodded and quickly ordered Peter to lower the shield. "Open the gate; raise the shield once the jumper arrives!"

Peter nodded, and then he lowered the shield and transmitted a signal through to Sheppard so he would now he was clear to come in.

-0-0-0-0-0-

Ford knew that it could be a mistake to open the gate into Atlantis like that, but there was something strange about the whole event. Major Sheppard hasn't been gone long enough to prepare a possible strike against the city from the other side.

And now, it looked like a potentially dangerous move but that could be the only option they had right now. Ford turned the corner to the jumper bay and noticed his team was still standing near the jumper. He quickly told them what they could expect and then told them to take up defensive positions.

-0-0-0-0-0-

John was getting really close to the gate when he heard Grodin's voice over the radio, "Major Sheppard, the shield has been lowered."

A sigh escaped his lips as he heard those words, knowing he wouldn't crash into oblivion. The jumper shook a little as it took a hit, but it was already entering the event horizon. Once on the other side, John noticed the gate room filled with people, both military and non-military. He opened the roof hatch to the jumper bay and all went automatic from there.

He was finally home. Yes, there was still a whole lot of mess to sort out, but John didn't really care. For some reason his mind seemed to be fully connected with him, since he started to feel incredibly tired and a stabbing pain shot across his ribs. He tried to ignore it, as he thought about what was going to happen next.

John landed the jumper in his rightful spot but waited for a moment. He could see Rodney and a bunch of soldiers outside in the bay. John took a deep breath and finally opened the rear hatch. He felt people coming inside the jumper and Lt. Ford's voice telling him to stay where he was. Then the young Lieutenant called Carson to the jumper.

John knew the soldiers were pointing their guns at him, he didn't care nor did he move.

Next thing he knew John felt a sharp sting going through his right arm. He looked at it and saw a red tranquilizer dart sticking out of his arm. He couldn't help but smile as he completely understood Ford's actions, but he knew there was no need for that. After all, he would've passed out in a couple of minutes anyway.

-0-0-0-0-0-0-

Ford had expected to find a Genii team inside the jumper, or maybe a sign of foul play but instead of all that it was just the Major in the pilot seat and Dr. Weir on the floor, looking like hell.

Ford knew that knocking Sheppard out had been the best option for now. He had remembered that Dr. Heighmeyer had restricted the use of a stunner so therefore he hadn't wanted to take any risks. He turned away from the Major and noticed Carson walking into the jumper. He went straight for Dr. Weir and as Ford could have guessed shock was written all over the doctor's face.

Rodney had followed Carson in and froze in the middle of his step when he caught a glimpse of Elizabeth on the floor.

He felt like his breath just got stuck in his chest. Elizabeth's face was covered in blood, indicating clearly someone had taken a hit to her nose. But Carson seemed to be more concerned about the injuries to her neck. Rodney continued his way into the jumper, making sure he wasn't in the way of the medical team and walked up to join Ford in the ship's cockpit. "What do you think happened?"

Ford was staring at John, his face set. He barely even shook his head as he answered Rodney's question, "I don't know? This is just..."

Rodney saw the incredulous look in Ford's eyes and finished for him, "...Unbelievable," Ford nodded. "Yeah," Rodney agreed.

Rodney took a closer look at John and noticed blood splattered all over his shirt. He really didn't like the sight of blood and John had plenty of it, like he had been in a shower of blood. He slowly turned the chair to look at John face to face. The amount of blood was truly impressive and Rodney hesitated. Most of the blood was splattered and couldn't have possibly been his, except on the left side of John's chest. Rodney carefully pulled John's shirt up a bit and saw a slash across his side, blood flowing freely. "Oh crap!"

"McKay?" Ford looked at Rodney and down to what the man was looking at. He immediately called for Dr. Beckett, who was preparing to leave with Weir. "Dr. Beckett, you better get in here."

Carson gave a few last instructions to a nurse beside him as they took Elizabeth out of the bay before he walked back towards Rodney and Ford. "What is it?" Ford pointed down at the gash and Carson didn't need a second to start his work on saving the Major from bleeding out. "Help me get him to the floor."

Ford helped Carson picking John up and placing him on the floor in the back of the jumper, where there was more space. As soon as he had the blood flow under some form of control, he escorted the Major out to the infirmary. Ford gave him two guards just in case.

-0-0-0-0-0-0-

About three hours later a small group of people had gathered outside the infirmary. They were all silently gazing at each other, trying to read each other's emotions. Rodney was pacing back and forth, only slightly working on the other's nerves.

After what had seemed like days, Carson finally walked out, looking tired and worried.

They looked anxiously waiting what he had to say. "They are going to be fine. Elizabeth's neck injuries indicate someone has tried to choke her but changed his mind at the very last minute. Her state is a bit delicate, but I'm confident she will make a full recovery. As for the Major..." Carson suddenly turned grim, "Physically, he will be fine. It was just a deep graze on his side. Mentally, however ... I'm not sure, that's not really my field. He's been awake for the past two hours and he hasn't talked, resisted, or insulted anyone. And he woke up when one of the nurses was cleaning his wound; yesterday he would've made a racket in there, today he just let her be."

"What about the blood?" Ford tried to look past the doctor but he couldn't see a thing.

"I don't know. The blood on his side was mostly his. I took a sample from the splatters but I don't think we will know who it is from until we've tested it. I don't think its Elizabeth's, if that's what you're wondering." The group released their breaths simultaneously, which they hadn't known they were holding.

Ford walked forward, "Can we see him?"

Carson hesitated, "Not now. Maybe tomorrow, there are a lot of people in there now." They nodded understanding the necessity for rest. Carson continued, "I'll keep you informed if anything changes."

They all left, except Rodney, who lingered a little longer, "Come on, Carson!" He started, "Let's just pretend that you have to change my bandage again."

Carson sighed and looked at Rodney, giving his request a minute or two, "Ok, I don't want you bleeding to death again."

McKay smiled and followed the doctor back into the infirmary. The number of occupied beds was impressive; they never had so many people in there at the same time. As they continued walking, Rodney and Carson walked by Kate's bed, she looked like she was just waking up.

Carson was instantly by her side asking questions about how she felt and if she were in any sort of pain. She replied drowsily and looked at Rodney, "What happened?"

Rodney and Carson briefly exchanged worried looks, while Kate took a moment to look around her and noticed Elizabeth lying in the bed next to her. Her neck was covered in dark bruises and her face was swollen. Kate covered her mouth, trying to hide a gasp.

Carson placed a soothing hand on her shoulder, "Calm down, she will be ok." She nodded barely visible, and already guilt started to build up inside her as she knew only man had been capable of causing those injuries.

Rodney immediately picked up on her guilt-trip and stepped in between Kate's and Elizabeth's bed. "This isn't your fault. If we have anyone to blame for this, it's the Genii."

"Kate, can you tell us what happened in the brig?" Carson said as he looked from Rodney to Kate. "How did Major Sheppard manage to escape from his cell?"

Kate closed her eyes briefly, seeing flashes of what had happened flash by. She shivered lightly and her eyes shot open at one particular bad image. "I..."

"Take your time." Carson squeezed her shoulder. "Just tell us what you remember."

Kate closed her eyes again and took a deep breath, "He was making progress, and I finally managed to get through to him. But the moment he didn't like things..." Kate's breathing quickened at the thought.

"Is ok, we can do this later." Carson assured her they weren't in any hurry, even though they kind of were.

Kate shook her head, indicating she could go on telling. "He began acting like John, he wanted to kill himself. I couldn't allow that to happen so I ordered the guards to open the cell and then ... then he took me hostage."

Rodney nodded, "He hurt you, and used you as a shield."

Kate nodded, tears shining in the corner of her eyes. She winced as a stab of pain went through her upper body. Carson quickly grabbed a syringe and emptied it in Kate's IV. "You'll feel better in a second. And Kate..." She gazed up at him. "It's not your fault; I would've done the same."

She nodded absentmindedly, the drug starting to work, and before she knew it she was asleep again. "Rest now. You'll feel better when you wake up," Carson said this more to himself than Kate, since she had already dozed off.

As soon as he was sure Kate was going to be fine for now, Rodney moved on towards Elizabeth. As he stood by her bedside it finally sunk in how lucky she was to be alive. She looked worse from up close. Rodney jumped as Carson materialized next to him.

"All we can do is wait. I can only guess that someone tried to choke her ... to death." Carson sighed. "I believe she could have suffered from hypoxia but we're not going to be sure of the extent of the damage until she wakes up. Now she is just unconscious. None of the tests revealed signs of brain damage or anything else alike. But whoever hit her in the face, hit target. Her nose is broken."

Rodney pulled his gaze away from Weir and looked at Carson, "Why do I think you and I, know who did this to her?"

Carson turned even sadder, "Because he's lying in the last bed behind that curtain." He vaguely pointed ahead and all Rodney had to do was follow the doctor's finger.

Rodney nodded and then started walking towards John's bed, leaving Carson who in turn went to his office, "Just stop by my office before you go."

"I will."

As Rodney approached the bed, his mind raced through a thousand possibilities to do and curses to throw at John. But deep down Rodney had no idea what he should say to the man that hurt so many friends and colleagues. As he passed the curtain, Rodney looked upon the man lying in the bed. "Hello Ignatius."

John stayed quiet, staring at some non-existent point on the ceiling. His face as expressionless as it could ever be. Rodney didn't give up after one try and said, "Ignatius?"

Still there was no response so Rodney turned to leave. But at that moment he heard a strong voice behind him. "Don't."

Rodney turned to face John, "What?"

John's sight went from the ceiling to Rodney, "Please don't call me that again." This time his voice sounded weak and defeated.

Rodney was momentarily confused, but he had heard that tone before, "Hi John, nice to have you back."

John's sight focused back on the ceiling, "Not so nice, I'm sorry ... about everything." He closed his eyes, indicating he was done talking and wanted to be left alone.

Even though Rodney wanted to ask a thousand questions, he nodded and left, stopping by Carson's office as he had promised. As he left Rodney wondered whether this was just a moment of clarity and he would wake up as Ignatius again, or if John was really back to his old self.


	16. Somewhere I Belong

**Somewhere I belong.**

Three days had passed since John had come back with Elizabeth. He had been moved back to the brig as soon as possible. Ford had been extra cautious, making the move as safe as he could. John had been hand-cuffed and had another pair of cuffs around his ankles, preventing any sort of escape. It had been swift and weird, because he had barely said a word and he hadn't fought or complaint about anything whatsoever. It had definitely been scary to see the Major like that.

Everyone had taken his behavior as weird and possibly fake, so they left him in the cell with no one feeling like visiting him any time soon, leaving him to himself. It was probably for the best to leave it like that for a couple of days, giving Atlantis the chance to return to a somewhat normal state of functioning.

If they were worried about John's mental state, they were even more worried about Elizabeth's physical and mental state. She had lapsed into a state of unconsciousness that had Carson on edge.

It took her a while but Elizabeth did finally wake up, though finding herself almost alone in the infirmary. There were others there with her, but none were awake. But not for long, Carson materialized by her side out of nowhere, startling her pretty good, asking her all sorts of questions, which she barely understood.

"Elizabeth, can you hear me?" Carson was pointing his penlight in her eyes, something she didn't seem to appreciate that much.

Elizabeth looked around confused and desperately tried to answer, but she couldn't. Her voice was barely audible and broken. Carson placed a reassuring hand on her shoulder, looking straight at her, "Stop, don't try to talk! Do you know why you're here, lass?"

Elizabeth blinked and then frowned, her mind drawing a blank as to the reason why she was in the infirmary. She shook her head lightly, causing Carson to frown lightly. "You don't remember?" Elizabeth's eyes darted wildly across the room as if looking for something and shook her head, yet again.

She could see Carson's mouth moving, and desperately tried to hear what he was saying but her mind was drifting into a black swirl and she knew no more. If it had been glorious oblivion, Elizabeth wouldn't have cared much she had lost touch with the conscious world, but to her own dismay her unconscious mind filled with images. The sound of a gun being fired ... Kolya and John talking ... John's eyes, murderous, and his hands in her neck... Elizabeth felt her life slipping away from her.

She had seen the change in his eyes, it had been sudden and strange. But Elizabeth knew no more, all that she knew was that his hands prevented her from breathing and that he was holding her down with every bit of strength he had.

But he had spoken with Kolya, and they had been on the Genii home world, and he hadn't allowed for any of the Genii to hurt her, while his hands were still in place, choking the life out of her.

John had been talking to Kolya and he had … killed him but at the same time Elizabeth saw John staring down in her dying eyes as she was pinned underneath his strong body. He was driven to kill and he would soon succeed.

Next thing she knew, she was screaming at the top of her lungs, fighting desperately for some air. Her eyes flew wide open and for a moment she was totally disorientated, until she found Rodney standing by her side, holding her down, fear clearly readable in his eyes. She tried to take a few deep breaths but failed miserably until Carson placed an oxygen mask over her nose and mouth. She could feel the much needed oxygen fill her lungs and relaxed back against the pillows, while Carson looked her over, checking her vitals and noting some things down on her chart. Not paying any attention to Beckett she turned her full attention on Rodney. "Where ... where is J-John?"

Rodney noticed her voice was barely louder than a whisper. He quickly exchanged looks with Carson before he replied, "He's back in the brig."

"I need ... to see him!" Elizabeth tried to get out of bed, ignoring all the wires and the IV-line, but Rodney firmly held her down. She immediately started struggling against his hold. All she wanted, was to see him and tell everyone what she knew, what she had seen.

"A little help here, please!" Rodney called for an extra pair of hands and was soon joined by Carson, who called a nurse over. The nurse picked up a syringe from a nearby table and injected it into the IV-line. Elizabeth kept struggling and fighting, until she felt how her entire body went limp. She whimpered softly as her world slowly turned into blackness once more.

Elizabeth had no idea how long she had been under thanks to the sedative, but when she woke up again she eased her mind to the waking world slowly, deliberately not warning anybody of her alertness to her surroundings. Her eyes moved around and she found Rodney sitting next to her bed, reading some paper. The moment he noticed she was awake, he put the paper away and got up. "Good morning!" He smiled. "How are you feeling?"

"How long since he took me?" Straight to the point.

Rodney crossed his arms over his chest and hesitated a little, "Five days."

"Where is he now?"

"He's in his cell. The order is to keep him there until we can figure out what happened and what to do with him now."

Elizabeth noticed Carson coming up to them, arriving mid-conversation. She turned back at Rodney, ignoring Beckett completely, a pleading look in her eyes, she hoped would do the trick. "You have to let him go, Rodney."

Carson and Rodney exchanged worried looks, "I don't think that's a good idea, love," Carson replied to her plea. "We have no idea what his mental state is at this very moment and the most qualified doctor who could tell us that is lying right next to you."

Elizabeth blinked and turned to her right side, seeing Dr. Kate Heightmeyer sound asleep. She had no idea how the doctor had gotten injured but she was pretty sure John was more than likely involved with it. Her eyes darted back to the two men. "No, you don't understand, he's back! John is back!"

Seeing both men didn't seem to be interested whether John was back or if they were still dealing with Ignatius, she decided to make her next move and threw her blankets back in order to swing her legs over the edge of the bed. But Carson anticipated the move and placed a gentle but demanding hand on Elizabeth's shoulder easing her back down and pulling the blankets back up. She resisted, pushed a little more and moved as if to stand up.

"What makes you think that?" Rodney decided for the best to show a little interest in what Elizabeth was claiming to know.

Elizabeth gave up and fell back against the pillow, staring at Rodney, "Please Rodney, talk to him. Believe me, he's back…." another thought popped into her mind and again she wanted to get out. "I need to see him."

Carson pushed her back down, glaring at her and almost threatening to sedate her again. "No, you need to rest."

"But I..." she winced as her brain had just found out how to turn the pain back on, and realized a little bit more rest couldn't hurt at all. She did, however, look back at Rodney, making sure he was going to see John. "Please talk to him! You'll see, he's really back."

Rodney only nodded and stepped aside to let Carson do a few last check-ups, as they noticed she was already dozing off again.

-0-0-0-0-0-0-0-

Later that day Rodney decided to give Elizabeth's plea a try, so he made his way down to the brig. A place that was now so full of bad memories that most people didn't really feel like going down there any time soon.

As Rodney walked into the room he noticed John sitting on the floor in the middle of his cell, staring off at some invisible spot on the wall opposite him. There was no longer a cot inside the cell, having broken his last one. And just for security reasons they had only given him a small mattress to lie on. Rodney started with a simple hello, but John didn't say anything nor did he look up to acknowledge McKay's presence. "I just came by to see how you were doing." Rodney bit his lip, still waiting for a response of sorts. "And to tell you that Elizabeth is going to be just fine."

At that, John slowly turned his attention on Rodney, letting his last statement sink in while he released a slow breath. "I thought I killed her."

"You nearly did." McKay took a chair and sat himself down in front of John. "Why did you take her?"

"I had to prove something." His voice monotonous.

Rodney glared, "Prove something? Right. So what should I call you now, Sheppard or Ignatius?"

This time it was John's turn to glare, unwillingly showing emotion in his eyes. "I am nobody. I am no longer the person you knew."

Rodney blinked, looking slightly confused, "What do you mean?"

"I don't care what you are planning on doing with me. I deserve worse than whatever it will be, but I can assure you that you will never, ever, see Ignatius again."

Rodney doubted that for a moment, since Ignatius had fooled them before. "What happened on the Genii home world?"

"I killed him."

"Who?"

"Kolya."

"Why?" Rodney couldn't resist to feel a bit relieved, knowing the man they all hated so much had finally been put down. But he couldn't help either to wonder what had caused his death.

"Because he is the reason I'm a monster."

Rodney remained silent, hearing John talk with such hatred, "It's not your fault; Major, nothing you have done is your fault. If we should be pointing fingers, it should be at us. We should have gone back to that planet for you. We could have done it and we didn't. So don't make yourself a martyr because we were the ones who left you behind. _We_ left a man behind, _you_."

John looked back at Rodney, "I already told you once ... it was never your fault."

"Not yours either."

John turned back at staring to the imaginary spot on the wall, "I will pay for my crimes."

"You already did," Rodney shook his head lightly, knowing he was talking to a wall. John was beating himself up mentally.

McKay remained seated, watching John closely as he stared. He had decided it couldn't hurt to tell the Major what had happened while he had been gone and how everybody was dealing with the situation. He knew that Sheppard was actually listening since he could once in while see a flicker of recognition in the man's eyes.

But none of it would make a difference in the end, since John knew that all those that had gotten hurt were Ignatius' victims and at the time it was in fact him who had done the hurting. It had been his body that had attacked those people. Essentially it had been him, and not someone else.


	17. Got the life

**Got the Life**

Elizabeth woke to the sound of soft talking; having no idea about the time or even if another day had passed. As she slowly opened her eyes, she felt like she could handle anything given to her. She felt stronger than the last time she'd been awake. She immediately tested her newly found strength and sat up straighter, holding the edge of the bed with one hand, making sure she wasn't going to tumble out. Thankfully there was no-one around, in particular Carson, for she felt her head spin like crazy. She carefully tested her legs and got on her feet, swaying only a little still holding the bed firmly.

She wondered why she had thought John had turned back to his normal self. It was weird since he had had in fact tried to kill her, though when he was choking her she had seen something in his eyes, something she had recognized before she had blacked out. Maybe the reason was that he had brought her back to Atlantis, not leaving her to the mercy of the Genii, and he had killed Kolya.

Elizabeth took a small step forward, her feet tingling from the cold floor. She steadied herself and took another step until she suddenly heard Carson's stern voice behind her, and she hadn't even made it to the curtain yet. "Where do you think you're going?"

She managed a small reply, though her voice was till hoarse. "I need to see him!"

Carson stepped up next to her, catching her arm as she swayed again. "I'm sorry, Dr. Weir, but I cannot allow you to go anywhere but back into your bed."

Elizabeth pulled away, "I'm well enough, Carson," she moved forward, away from him. She so desperately wanted out of the infirmary that she was more than willing to risk a chance to get sedated again. After all there were memories, feelings and facts that needed her attention; she was the only one who could do something about them.

Carson wasn't just going to give in and stepped right in front of her, effectively blocking her way.

"Please Carson, I have to see him. I need to speak with him."

Carson felt his heart sink at Elizabeth's pleas. He had never seen so much pain in her eyes as he saw now. She was so badly trying to convince him while he and the others had yet to figure out what had happened between her and the Major when John had taken her.

Since her verbal pleas didn't seem to be working much she once again tried to walk passed him, but Carson stopped her. Elizabeth knew Carson meant well, but she knew that if John was really back she would be the one person who could convince him that the atrocities he committed as Ignatius weren't his fault. She was positively sure that the reality of what had happened to him and what he had done while being Ignatius were going to be a severe shock.

Elizabeth knew that if that were the case, then John Sheppard would never forgive himself. And they hadn't come this far to loose him in the end. Elizabeth pulled her final card as she looked straight at Carson, "Carson, please, I just need to see him. I'll be down at the brig for only a few minutes. Please?" She kept staring at him, wondering briefly what was going through his mind. "Please, say something? If you want, you can sedate me until the end of next month but please, just let me see him."

"Elizabeth, as much as I would want to le you go and see him. We don't know how Major Sheppard is doing mentally right now. We don't know how he will react to your presence. Ignatius may not like it," Beckett tried his best to persuade her it was better to wait a while longer, so Kate Heightmeyer had a chance to see him first. And since she was going to need some time to recover, Weir would get some well-earned rest too.

"But that's the thing Carson, there is no more Ignatius. You have to believe me!"

Carson seemed to be thinking about it, though he was still against her going down to the brig. Elizabeth wasn't fit for anything right now, but before he could form a reply, Rodney walked in, "I'll go with her."

Elizabeth and Carson were both startled, but before Carson could give Rodney a solid reason to restrict Elizabeth from seeing the Major, Rodney tackled him with a reason she should see the Major. "Ever since he came back, he hasn't had any outbursts, no threats, not even a request. Nor has he talked in anyway like Ignatius."

Carson threw Rodney a skeptical look, "What if he's faking it? He's done it before."

Rodney shook his head lightly, "I don't think so, not this time."

"What makes you think that?" Carson asked.

"If he was faking it, by now he would have gotten tired of the show. Instead, if you go talk to him, Sheppard will only say how much he deserves to be where he is now."

Carson nodded almost unnoticeable, "Ok, but no longer than ten minutes, got it?" He turned to face Elizabeth again, "After that I want you back up here."

Elizabeth nodded eagerly and Rodney helped her into a wheelchair, wheeling her out of the infirmary and straight down to the brig. They moved in silence, though Rodney wanted nothing else but to ask her what had happened when John had taken her. But he decided against it, since it wasn't the time or the place to ask her, not yet anyway.

When they arrived at the cell, John was still sitting on the floor, still staring off into space. But once he caught sight of Elizabeth out of the corners of his eyes, he got up and stared at her. There was no anger in his eyes, but sadness and guilt.

Elizabeth had colorful bruises on her face and in her neck where his hands had made contact. Her nose was still a bit swollen and he had been right assuming he had broken it. John whispered, "I thought you were dead," he looked around the room and lowered his head, repeating even more softly, "I thought you were dead."

Elizabeth didn't say a thing but her face was set. She looked up at Rodney and broke the silence, "Open the cell!"

Everyone, including John, looked at her in surprise. Rodney grabbed her shoulders, "What are you doing? Have you lost your mind? We're still not sure about his..."

Elizabeth pulled away from Rodney, "You're not, but I am. Now..." She almost glared at the guards, "...I order you to open the door."

Her order went through this time and the airman in charge opened it up. Once the door was open, John stayed frozen on the spot. He just stared at Elizabeth, amazed that she would take such a risk when he couldn't even trust himself.

She didn't move at first, but after a moment she slowly got up out of the wheel chair and walked inside the cell, not even swaying once. Rodney kept close behind her just in case her legs suddenly decided to give out from under her. Elizabeth walked straight towards John and slapped him in the face. Everyone was stunned by her actions. But no one even dared to move when she did it again.

John didn't react in any sort of way.

When she was done slapping him, Elizabeth continued, "That is for what you did." She waited a moment, "Who are you?"

John stared at her, a bewildered expression on his face. When she noticed he wasn't going to answer, Elizabeth slapped him again, "I asked you a question! Who are you?"

John didn't know what she was doing but if he wasn't going to answer quickly, he would be receiving another slap. He could still feel her hand on his cheek, and when he saw another slap coming, he grabbed her wrist halfway. Not too hard, as not to hurt her but to stop her. Within seconds every soldier in the room had its gun pointed at John.

Elizabeth's heart-rate doubled in speed and she had to admit that she felt pretty scared for a moment. But when he spoke, she relaxed. His words came out softly and there wasn't a sign of anger or confusion in his face, "Major John Sheppard, United States Air Force... do you want my serial number too?"

Elizabeth relaxed and for a moment she felt like she could accomplish anything until she felt Rodney's arms steady her. "I should get you back to the infirmary. Don't want Beckett to sedate you again to force some rest onto you." Rodney started pulling her back out of the cell and into the waiting wheelchair.

She looked straight into John's eyes, and then addressed the guards, "Take him to his quarters and place a guard in front of his door."

With that Elizabeth allowed Rodney to fuss over her and wheel her back to the infirmary and the warmth of her bed and a few hours of rest. Before they left she looked at John one last time. "You won't be punished for what happened, but... I hope you understand, John. The guards will be with you for a while, and I hope you're up to it. There's a job to be done in Atlantis, a job that you're meant to do."

As the words sank in, she and Rodney left, leaving a very confused John Sheppard in her wake.


	18. Reanimation

**Reanimation**

Elizabeth wasn't sure whether she had just done the wrong or the right thing. She was absolutely sure John was back and for her that was enough. She knew, though, deep in her heart that she had done it just to give back the trust John deserved, making sure he knew he was no longer trapped inside a terrible nightmare. He was given an opportunity to get back to normal. Elizabeth knew that he had a very long road ahead. It had to start somewhere, no matter the doubtful stares everyone had. Even Rodney was filled with doubt but he had decided to remain silent for now, quietly pushing the wheelchair back to the infirmary.

As soon as they were back in the infirmary Rodney helped Elizabeth into her bed, while Carson reattached an IV line and tucked her in, making sure she wasn't going anywhere any time soon. An uncomfortable silence accompanied their actions, and the trio stared at each other as if waiting for something. They all knew what was in each of their thoughts.

"Elizabeth has released Major Sheppard to his quarters." Rodney eventually broke the silence.

Carson gazed at Rodney in surprise and then turned to Elizabeth, "You did what? Why? How can you be..."

But Elizabeth cut him off, "I want to make something absolutely clear here. If anything should happen, I will claim full responsibility. It was, after all, my responsibility when he was kidnapped."

Hearing Elizabeth trying to take the blame of what had happened Rodney, in turn, cut her off, "You are not responsible for that."

"Yes, I am Rodney. And you know it. I didn't allow for you to return to the planet," Elizabeth's gave McKay a stern look, telling him not to argue the point. "But for now John needs us, and everyone must help in any way possible. I can understand that it won't be easy, he did hurt a few. But we can't turn our backs on him for something that was out of his hands… out of our hands."

Rodney sighed, knowing Elizabeth was right. He, after all, had seen it the moment he had talked with John. Carson didn't reply but stuck to nodding his head instead. The doctor knew Elizabeth was right.

"How's everybody?" Elizabeth subtly changed the subject away from John to Ignatius' victims.

Carson gave her a small smile, "Sgt. Stackhouse will be released tomorrow, while Airman Cortez may be released to his quarters the day after. Sgt. Hatfield is stable and recuperating and Dr. Heightmeyer will be ok."

Elizabeth sighed. It felt good to know that no one died because of Ignatius. She finally allowed her body and mind to relax, for the first time in so many days, and leaned back on her pillow. Carson and Rodney smiled as they watched her doze off into a dreamless sleep, finally allowing her to rest to the fullest.

-0-0-0-0-

John was numb. Numb when they had escorted him to his room. Numb when he had walked in and discovered that the room was still intact. Numb when a couple of days later Rodney, Teyla and Ford had come by his room to visit and to tell him that Elizabeth had been released from the infirmary. To inform him that everyone still confined to the infirmary was recuperating well and would be ok.

He still felt numb when a week later Elizabeth had walked into his room to talk about what happened. He had talked... a bit anyways and somehow they had come to terms, making it possible for him to move freely around Atlantis. He knew they would have to talk again someday, since this kind of event was not easily forgotten.

John had managed to get his hands on a razor and had shaved at the first opportunity he had gotten. Seeing his face with the beard felt like giving Ignatius a face, which was something to remember him by and as a result hate himself.

The numbness only got worse every time he passed by someone he had hurt. He had managed to make a public apology for what had happened and no one had shown any signs of anger or resentment towards John. In fact after he was allowed to live normally, everyone on base took a moment to let him know that he was welcome and still one of their own. He appreciated the way they handled him, especially those close to him, at any chance possible Teyla would make an appointment to train with him in order to keep his mind occupied. Ford and most of the soldiers had taken the task of recreation, calling him to movies, poker games and anything fun related. Sometimes some of the scientist would join in the poker games or in heated discussions over sport-related topics.

Rodney had taken the task of checking on him once in a while to make sure John didn't spent too much time alone. Elizabeth kept her distance for a while, she mostly joined him for lunch or dinner to make sure everything was ok. But as much as everyone tried, John had managed to completely evade Kate Heightmeyer.

John knew she had talked with everyone close to him, and he was sure that she had employed Rodney as his shadow.

There were times that John felt like nothing of it had really happened and it had just been an ugly nightmare. Everyone was ok, and the Genii never caught him. But then there were the bad days, when he barely walked out of his room. And when he did, he felt like everyone was just waiting for him to break, to become Ignatius once again.

It had been 3 months since he had come through the gate calling himself Ignatius. He was still jobless and hiding. Currently he had picked a particular spot out in his room, the floor between the bed and the wall. If anyone walked in, John was sure they wouldn't see him there and would walk away again.

At that moment the door opened and Elizabeth's voice could be heard, "Good Morning John."

John didn't move nor look at her when he replied, "How did you know I was here?"

Elizabeth sighed, the smile gracing her features pouring itself into her voice as she answered, "Because I can see your feet."

John sat up, looked at Elizabeth and then down to his feet, which were sticking out at the end where his bed stopped. He shrugged and got up to sit on the bed instead.

Elizabeth moved further into the room and looked around. The wall, which with once held a Johnny Cash poster, was now stripped bare and the poster lay crumpled in a corner on top of a cardboard box, which seemed to hold a couple of John's personal belongings. Now that she noticed, she realized there was nothing around the room that could tell her it was in fact the room of Major John Sheppard. The desk was empty and the bed was unmade. It hit her that it felt as if John had had a recent outburst, including a broken picture sticking out of the box. Elizabeth grabbed a nearby chair and sat down in front of John, "How much longer?"

John stared at her in confusion, "What?"

"How long until you stop pitying yourself?"

John lowered his head and answered a bit annoyed, "Elizabeth, not again!"

Her face was set and determined, "You need to talk about it! John, believe me, once you let it all out, it'll be much easier to let go. It's been three months, I'm not pretending that you have to get better tomorrow, but at least I want to see you doing something about it!"

John felt anger rise with every passing second, "It's really easy to say it..."

Elizabeth cut him off, "Then do it! Let it out! It has to be better than wallowing in self pity all day!"

At that point John snapped, and shouted as he stood up, "And what do you want me to do? You want me to tell you and everyone else that I remember everything, that I can remember every single detail Kolya did to me! That I remember shooting Rodney, Ford, Bates and the list goes on! That I remember that I tried to kill you and that I came really close to actually succeed! Is that what you want me to say? Well there, you just heard it! Why don't you just leave me alone from now on?"

Elizabeth sighed and stood up, facing John, "John, do I have to remind you that you already apologized to everyone when you didn't have to. And that all those people understand. I know for sure that no one is holding a grudge against you. They still want to work with you. Yes, it won't be easy. Yes, it might be awkward at times, but in time you'll see that things can get better."

Elizabeth noticed John relaxing a bit, and she continued, "John, you don't have to do this alone. I am your friend and even though you can be annoying and stubborn at times, I would really like to see you back on duty. Who else but you is going to keep Ford from naming things or keep Rodney in check while being off-world? Just look around and you'll find that there are a lot of people in this city that care for you and are willing to help you through this. All you have to do is give them a chance. I know I did, because if I hadn't you would still be trapped inside the cell on the brig."

Elizabeth could tell from his face John was touched by what she had said. But then he shook his head, "I'm sorry, Elizabeth, but I don't think anyone can save me now." He turned around, and stormed out of his room.


	19. Don't stop dancing

**Don't stop dancing**

Rodney was so concentrated on his current project, a newly found ancient object of which he had no idea what it was supposed to do, that when Elizabeth walked into his lab he didn't even noticed her. Until she coughed a little to make her presence known to him, startling him in the process. He quickly added a few notes to the open file on his laptop before he looked up at Elizabeth, who had taken a seat across from him. She was wearing a grim expression across her features.

"I'm guessing it didn't go as well as you had hoped it would go?" Rodney asked

Elizabeth briefly dropped her head in her hands before glancing back at Rodney, "I don't know what else to do. I'm coming up shot to just bang him in the head with something and see if he reacts."

Rodney gently placed his object down and turned his full attention to the desperate diplomat, "Where is he?"

"Wherever he goes when he disappears."

"I think I might know where he is. Do you want me to talk to him?"

A tired look was visible in Elizabeth's eyes as she looked at him, almost pleadingly. "Could you?"

Rodney assured himself the ancient object was safely tucked away, and the file on his computer saved before he got up and walked over to the door. "I might as well bang him in the head myself. And I really need Kate off my back; he's been evading her for too long now."

Elizabeth smiled as she followed him, "Thank you, Rodney, just let me know when you find him, okay?"

Rodney nodded and they both left the lab, each turning in a different direction. Rodney knew it wasn't a matter of finding John, he knew perfectly well where John would be hiding out; at the top of the Southwest pier.

-0-0-0-0-0-

John was feeling so tired. The only thing he wanted so desperately was to feel okay again. The Southwest pier was far away from everything and everyone, there were no stares, no people taking pity on him, no whispers behind his back. He liked it there, sitting on one of the steps on the balcony, facing the ocean, with his side resting against the rails.

Every time he was there, in his favorite spot these days, time would fly by. He would never have a clue how long he'd sat there, listening to sound of waves crashing against the city.

As he focused on the sound of the waves and the ocean, it made him forget of what awaited him once he'd return back to civilization. He was interrupted in his brooding as he heard the door open and close. He knew his time of peace was once again over. It was only a matter of time before someone came looking for him anyway.

It was always someone different, Ford or Teyla or Elizabeth. John turned his head towards the door, acknowledging the person who was standing behind him. Today it was Rodney.

Rodney walked out to the balcony, moving straight towards the rails, as if he was just there to have a look at the view. He ignored John completely, acting as if he wasn't even there.

John stared at Rodney, waiting for the argument to come, but Rodney remained silent. John wasn't in the mood for games, of any kind, "What do you want?"

Rodney turned around to face John, "Do you remember the first time I came to see you... when you were still acting as Ignatius?"

John glared at Rodney for bringing the name up in his question, "What about it?"

Rodney crossed his arms over his chest, "Do you remember what I called you that day?"

"You called me many things that day."

"No, you must remember since you told Elizabeth that you do remember everything you did as Ignatius. It was the first thing I called you. But the funny thing is I never thought I would have to say it to John Sheppard as well."

John frowned and then his glare went up a notch, "Don't do it!"

"You're acting like one!"

"No, I'm not!"

"Yes, you are!"

"No, I'm NOT!

"Yes... you... are!"

John's glare disappeared at once but was immediately replaced with frustration, "I'm not a coward, Rodney."

"Then please enlighten me, what exactly are you doing here?"

John looked out towards the ocean, "I wanted to get away, I needed to be alone."

"You're hiding, which in my opinion, not that it matters much to anyone, is a cowardly action."

John just snapped, "Stop it, Rodney!"

"Then tell me why you are evading Kate Heightmeyer?"

John suddenly got up, startling Rodney a little, "I attacked her, Rodney! And you want her to analyze me? What I did to her is not something you easily forget!"

Now it was Rodney's turn to let his temper loose a little, "You attacked Elizabeth and you shot me! We could have turned our backs on you and leave you to rot in guilt. Which you seem to be doing anyways. It's just that you don't want to talk about what happened. We all had to do it, it has affected a lot of people, but you are sooooo strong. You can deal with it alone. Bullshit! Explain to me how your recent behavior is not being a coward."

"Rodney..."

"No! Don't Rodney me! If you would use that goop you have for a brain, you would know that there is nothing wrong with getting help. What I'm saying is that the SGC had to deal with situations like this, but everyone involved always came back to normal. You know why?" Rodney waited for John to say something, but he was met with silence, so he continued, "… they knew that what had happened to them was beyond their control and that their lives had to continue. They returned to a somewhat normal life every time but they could never do it alone, they always needed someone's help to do so. You can try as hard as you might but somewhere along the line you need all the help you can get."

John slowly shook his head and turned his gaze to the floor, "It's not the same, Rodney."

Rodney closed in on John, "Yes, it is completely the same thing. The only difference is that you haven't accepted that there was nothing you could do to prevent what happened. You caused some damage, yes. But now it's time to return back to that somewhat normal life of yours."

John ran his hand through his hair and replied, "It's not the same! How can anyone expect me to act like nothing happened when I almost killed you, after I almost raped and killed Elizabeth? I injured a lot of people Rodney. I can't do this!"

"You can't do this! You selfish coward!"

John snapped completely at that and roughly grabbed Rodney's shirt and pushed him against the rails. The move reminded Rodney of one particular day when Kolya had done exactly the same thing, pushing him against and almost over the railing. He shuddered as he remembered that, while at the same time he could feel the rails poke in his back, sensing they were not particularly happy with the weight pushing against them. Rodney held on to John for dear life. "Sheppard! Let me go!"

But John didn't hear him, his face was all screwed up in rage, "You have no idea! None of you do!" John was screaming at the top of his lungs, "I can't do it! Every time I go to sleep all I get is nightmares! Every time I see someone I hurt, I know they don't want to be near me! Every time I look in the mirror all I see is HIM! His thoughts ... what he did ... what he dreamed of doing! I may have killed Kolya, but I can still see him mocking me, knowing that I will never be the same again... EVER!"

Rodney listened to John, finally getting what was eating at John's mind. The rail swayed again and he tightened his grip on John, but with every second that passed, John seemed to be pushing him more and more towards the edge. Things were getting a little desperate, and Rodney didn't really felt like waiting until John had calmed down. But John didn't seem all too eager to calm down and at once Rodney acted out of instinct and punched John square in his face. Sending them both back to the floor, where John landed on his butt while Rodney sank down grateful they hadn't fallen to the other side.

Rodney pulled himself up, holding onto the railing with his right hand. John was still on the floor, bewilderment was spread across his face and blood started to from his nose. "You hit me!"

Rodney cracked his fingers, trying to release some of the pain caused by the punch, though never taking his eyes off of John, "You tried to kill me!"

John stared off into space, his mind trying to grasp what had just happened. Rodney noticed John's expressionless face, but the tears that were slowly making their way down betrayed his hidden feelings.

John felt the warm tears slide over his cheeks. If this would have been any other day, he would have managed to keep himself in check, but not today. Not with what had just happened with Rodney. John slowly pulled his knees to his chest and lowered his head. He wanted to scream, he wanted so much to feel at peace once again. He wanted nothing more than to remove the memories that haunted him every night.

Rodney saw John's reaction and moved closer towards his friend. He sat down next to John but didn't say a word. He could tell from John's shaking, he was releasing his current frustrations. Rodney looked at his hand and realized it didn't hurt anymore. He took another look at John and patted him on the back, "Will you go and see Kate now?"

That seemed to snap John back to reality, as he looked up at Rodney, "I... Rodney..."

In turn Rodney didn't say a word but just stared at John.

John relaxed for a moment, breathing deeply, "Ok! But when I do, you will leave me alone again, right?"

Rodney relaxed and got up, "I will leave you alone the moment you're back on duty. Now, you can't tell me that you're going to see the doctor and then bail on me!"

John was quiet for a minute before he replied, "Ok."

Rodney offered his hand to John and helped him stand up, "Good! Come on, I need to drop you off at Carson's infirmary first. He'll have my head for this."

Once on his feet John frowned, "Why?"

Rodney stared back, "You're bleeding."

Up to that point John hadn't noticed his nose had been bleeding, leaving blood all over his face. He touched his nose and winced, realizing that what Rodney said was true. "Don't worry about your head, Rodney."

"Why not?"

John turned around and started walking towards the door, "Just think of the biggest needle you can imagine."

Rodney saw John tilting his head back in an attempt to stop the bleeding, while he could hear a faint chuckle. He smiled. Even if John didn't want to see it yet, things could get back to normal if he really wanted to. But at the same time he couldn't help but think of that really big needle and he winced inwardly. Why did he hit John again? Oh yeah, to save his life, then he guessed the needle was worth it.

The walk back to civilization was done in silence, which was more than understandable. After his fight with Rodney, John knew that the maniac inside of him was gone for good.

When they finally walked into the infirmary, they found Elizabeth there talking with Carson. But when the doctor noticed John's state of mind and his face, he could barely control himself, "What happened?"

Rodney glanced at Elizabeth and replied, "I had to hit him in the head."

Elizabeth's mouth dropped in surprise. "Why?"

John then answered before Rodney could reply, "It was just a difference of opinion." John looked from Elizabeth to Rodney and back. "Nothing more."

Carson glared at Rodney, while he patted on one of the beds. John hopped onto it and let the doctor prod his nose.

Elizabeth glanced at Rodney and smiled, Carson noticed their exchange and wanted in on the situation, "What are you two smiling about?"

Elizabeth suddenly found the floor very interesting as she softly chuckled, "Well, it's just that I told Rodney that I wanted to hit John over the head, just to see if he would react."

John gave Rodney and Elizabeth a nasty glare. Therefore Rodney quickly added, "Remember what we talked about! You can't back out now!"

John's glare disappeared somewhat, while he allowed Carson to fix his bleeding nose.

-0-0-0-0-0-

John was glad Rodney didn't break his nose, but he had come darn close to it and as a result he was now sporting a nice bruise in the middle of his face. To be honest, John didn't want to go where he was heading to at the moment. But there wasn't any other choice, John knew that every person that passed by him, was a witness. And if he bailed now, the high hierarchy of Atlantis would know about it within the hour. He would never hear the end of it.

So, he continued walking and when he finally arrived at his destination, he just stood there looking at the door, suddenly finding the door extremely fascinating. He was on the verge to just turn around and leave, but at the same time he changed his mind and faced the door once more. He then turned to leave again, but just as he turned around the door opened and he could hear Dr. Heighmeyer's soft voice calling out to him, "Major Sheppard, I've been expecting you for a while. Rodney called me to be ready for you."

John flinched but turned around anyway to face her. Once Kate got a good look of his face, she gasped in shock, "Oh my God, Major, what happened to your face?"

John gave her a small smile, "I was discussing something with Rodney. We couldn't agree and things got a little out of hand."

"Are you ok?"

John shook his head dismissing it, "Yeah, Carson took a look at it. Not broke, just bruised."

Suddenly John looked as if he wanted to run away. Kate smiled and moved away from the door, "Why don't you come inside so we can begin."

John hesitated for a minute but then walked into the office anyway. As he walked in she closed the door and poured herself a cup of coffee. Kate motioned the coffee to John, "Do you want some too?"

John was staring out the windows and turned to look at Kate, "Nah, I'm fine."

Kate walked with her cup of coffee towards the couch and motioned for him to do the same, "Shall we begin?"

John gazed down at Kate as she motioned him to sit. John sat across from her, already feeling uncomfortable. She seemed to notice it in his face, because she decided to break the ice, "How have you been feeling?"

"Okay, given the circumstances."

Kate took a sip from her coffee and placed the cup on the table in front of her, "I wanted to tell you, if we had done this sooner, things would've probably been different."

John looked puzzled, "What do you mean?"

Kate looked down, fidgeting a little with her hands, and then turned her gaze back to John, "I'm not sure I was ready to help you... let's just say that this is as much healing for me as it is for you."

John suddenly felt at a loss for words, and the only thing he could say was "I'm… sorry."

Kate shook her head, "It's not your fault, no matter what you've been saying."

John suddenly felt a familiar tightness in his chest, he wanted to get out of the office, he stood up and turned to the door, "This was a bad idea."

Kate got up too and grabbed John's arm, "No, it's not! If it was, you wouldn't have come here in the first place. Besides, you need this. Not only for your mental health, but for getting back to work."

She had hit a soft spot and John knew it. She let go of him as soon as he turned back to the couch.

Kate stared at him while she sat back down, "Where do you want to start?"

John looked at the woman and even if she looked as if nothing had happened, he knew that underneath she was still feeling the pain of that day, and the scars would always be a reminder of what had happened.

Maybe Rodney and Elizabeth were right. Maybe talking about it would help. John had been repressing everything in the hope of being able to live with it, without giving it too much thought. He spent the last three months like this and he felt tired. He didn't want to do that anymore. And he was already dead bored because of it.

Elizabeth had made it very clear; he would not get his job back until Kate had given him the all clear. He stared at Kate and knew she was going to wait until he was ready to talk and to let go. _Maybe this will go well, maybe anyways._

There were things that he still resisted to admit to himself, things that Kate would sense and would want them to surface. But that was for other days, other moods and today he didn't feel like dwelling on those particular moments. He knew that he would have to deal with everything at one point or the other, but he was now here and tomorrow was something he avoided for now, so he looked out the window and back at Kate, "Ask away!"

Kate smiled and opened a small notebook on her lap. John was still not sure about this, but as of now he felt like giving it a try. Maybe it would go well, maybe it wouldn't. He didn't know. But because of it, he knew that there were others that were willing to help him, when bad days arrived.

Although he knew that he would never forgive himself for what had happened. Maybe some day, he would start to forget bit by bit and maybe one day even, he would be able to forgive himself. But that was just wishful thinking, and John knew it, just as Kate asked her first question.

The End.

-0-0-0-0-0-

A/N: It was always my intention to make a little sequel for this fic, but the inspiration never settled. But now, as I went through the story to post it here. The bunnies are teething… let's see how that goes. :D I hope you enjoyed it and thanks for the reviews.


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